CanA coordinates calcium during cannula-fiber assembly (ASSEMBLY)
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Pyrodictium CanA binds calcium ions and undergoes donor-strand complementation to assemble hollow extracellular cannula fibers that extend from the cell envelope and participate in a cell-surface network.
Subject
Predicate
Object
Evidence
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Pyrodictium CanA binds calcium ions and undergoes donor-strand complementation to assemble hollow extracellular cannula fibers that extend from the cell envelope and participate in a cell-surface network.
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Object
Evidence
CanA cannula glycoprotein
coordinates
calcium ion
DOI:10.1038/s41467-025-64120-8 Sleutel et al. 2025 resolved calcium-bound CanA interfaces in self-assembled archaeal cannulae.
ATP-driven basal assembly builds and rotates the archaellum filament (ASSEMBLY)
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Prearchaellins are processed and added to the base of a helical filament by an ATP-powered ArlI/ArlJ motor. ArlH and lineage-specific scaffold proteins organize that motor, envelope proteins anchor it, and motor-driven rotation of the assembled filament propels archaeal cells.
Subject
Predicate
Object
Evidence
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Prearchaellins are processed and added to the base of a helical filament by an ATP-powered ArlI/ArlJ motor. ArlH and lineage-specific scaffold proteins organize that motor, envelope proteins anchor it, and motor-driven rotation of the assembled filament propels archaeal cells.
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Object
Evidence
PibD/FlaK prepilin peptidase
matures
prearchaellins
DOI:10.3389/fmicb.2015.00023 Albers and Jarrell 2015 review class-3 signal-peptide processing of prearchaellins by PibD or FlaK-like enzymes.
mature archaellins
polymerize into
archaeal-type flagellum
DOI:10.1038/s41467-022-28337-1 Gambelli et al. 2022 resolved the Methanocaldococcus villosus filament as a polymer of alternating ArlB1 and ArlB2 archaellins.
ArlX/ArlCDE cytosolic scaffold
organizes
ArlI/ArlJ motor core
DOI:10.1074/jbc.M112.414383 Banerjee et al. 2012 showed that FlaX forms oligomeric rings and interacts with FlaI in the Sulfolobus acidocaldarius motor.
DOI:10.1038/s41467-022-28337-1 Gambelli et al. 2022 summarize the Crenarchaeota versus Euryarchaeota ring modules surrounding ArlI/ArlJ.
Internal-core proteins organize a polar adhesin-bearing attachment organelle (FUNCTION)
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HMW2, P65, and HMW3 organize the terminal button and paired plates of the internal core. The polar extension positions P1/P40/P90 and P30 adhesins on the surface, coupling cytadherence with attachment-organelle-dependent gliding.
Subject
Predicate
Object
Evidence
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HMW2, P65, and HMW3 organize the terminal button and paired plates of the internal core. The polar extension positions P1/P40/P90 and P30 adhesins on the surface, coupling cytadherence with attachment-organelle-dependent gliding.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Basal-body rings couple ion-driven torque to the rod (FUNCTION)
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FliF forms the MS ring scaffold, the export gate occupies its center and builds the rod, LP rings let the distal rod spin through the Gram-negative envelope, and stator units apply torque through the C ring.
Subject
Predicate
Object
Evidence
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FliF forms the MS ring scaffold, the export gate occupies its center and builds the rod, LP rings let the distal rod spin through the Gram-negative envelope, and stator units apply torque through the C ring.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Evidence
MS ring
nucleates assembly of
bacterial-type flagellum basal body
DOI:10.1038/s41467-021-24507-9 Kawamoto et al. 2021 support the MS ring as a basal-body core and template for flagellar assembly.
C ring
assembles on
MS ring
DOI:10.1038/s41467-021-24507-9 Kawamoto et al. 2021 analyzed C-ring symmetry in native Salmonella basal bodies relative to the FliF MS ring.
flagellar type III membrane export gate
is housed by
MS ring
DOI:10.1038/s41467-021-24507-9 Kawamoto et al. 2021 linked the 23-subunit core of the M ring to a pore sized for the flagellar protein export gate.
FliG/FliM/FliN assemble into the torque-switching C ring (FUNCTION)
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FliG, FliM and FliN assemble into the C ring on the MS ring, stators apply torque through FliG, and phosphorylated CheY binds primarily to FliM to bias switch-complex conformation.
Subject
Predicate
Object
Evidence
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FliG, FliM and FliN assemble into the C ring on the MS ring, stators apply torque through FliG, and phosphorylated CheY binds primarily to FliM to bias switch-complex conformation.
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Evidence
bacterial-type flagellum basal body, C ring
assembles on
bacterial-type flagellum basal body, MS ring
DOI:10.1073/pnas.89.14.6304 Francis et al. 1992 placed the FliG switch protein on the cytoplasmic M-ring face of the basal body.
DOI:10.1038/s41467-021-24507-9 Kawamoto et al. 2021 measured C-ring symmetry relative to the FliF MS ring in native Salmonella basal bodies.
FliG
forms upper layer of
bacterial-type flagellum basal body, C ring
DOI:10.1038/emboj.2011.188 Paul et al. 2011 mapped FliG above FliM and FliN in the Salmonella flagellar rotor architecture.
FliM
forms middle layer of
bacterial-type flagellum basal body, C ring
DOI:10.1038/emboj.2011.188 Paul et al. 2011 mapped FliM beneath FliG in the flagellar rotor architecture.
FlgG forms the distal basal-body rod segment that adjoins the proximal rod, completes the central rod, and runs inside the Gram-negative LP-ring bushing.
Subject
Predicate
Object
Evidence
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FlgG forms the distal basal-body rod segment that adjoins the proximal rod, completes the central rod, and runs inside the Gram-negative LP-ring bushing.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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FlgH builds the outer-membrane L-ring bushing (FUNCTION)
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FlgH oligomers form the L ring at the outer-membrane side of the distal rod. The L ring and P ring form the LP-ring bushing that supports flagellar rod rotation.
Subject
Predicate
Object
Evidence
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FlgH oligomers form the L ring at the outer-membrane side of the distal rod. The L ring and P ring form the LP-ring bushing that supports flagellar rod rotation.
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flagellar L-ring protein FlgH
oligomerizes into
bacterial-type flagellum basal body, distal rod, L ring
DOI:10.1038/s41467-021-24715-3 Yamaguchi et al. 2021 built an atomic model of the Salmonella LP ring assigning FlgH to the L ring.
bacterial-type flagellum basal body, distal rod, L ring
FlgI builds the peptidoglycan P-ring bushing (FUNCTION)
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FlgI oligomers form the P ring around the distal rod. The P ring associates with peptidoglycan and cooperates with the L ring to make the LP-ring bushing that supports flagellar rod rotation.
Subject
Predicate
Object
Evidence
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FlgI oligomers form the P ring around the distal rod. The P ring associates with peptidoglycan and cooperates with the L ring to make the LP-ring bushing that supports flagellar rod rotation.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Evidence
flagellar P-ring protein FlgI
oligomerizes into
bacterial-type flagellum basal body, distal rod, P ring
DOI:10.1038/s41467-021-24715-3 Yamaguchi et al. 2021 built an atomic model of the Salmonella LP ring assigning FlgI to the P ring.
bacterial-type flagellum basal body, distal rod, P ring
FliF builds the membrane MS-ring platform (FUNCTION)
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FliF oligomers form the MS ring in the cytoplasmic membrane. The resulting ring anchors the basal body, templates C-ring and export-gate placement, and couples to the axial rod through FliE.
Subject
Predicate
Object
Evidence
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FliF oligomers form the MS ring in the cytoplasmic membrane. The resulting ring anchors the basal body, templates C-ring and export-gate placement, and couples to the axial rod through FliE.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Proximal rod proteins connect the motor to the distal rod (FUNCTION)
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FliE, FlgB, FlgC and FlgF form the proximal basal-body rod segment that links the motor-proximal FliF/MS-ring side of the basal body to the distal FlgG rod.
Subject
Predicate
Object
Evidence
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FliE, FlgB, FlgC and FlgF form the proximal basal-body rod segment that links the motor-proximal FliF/MS-ring side of the basal body to the distal FlgG rod.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Rod proteins assemble the axial drive shaft (FUNCTION)
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FliE, FlgB, FlgC and FlgF form the proximal rod and FlgG forms the distal rod. Together they make the central basal-body rod that spans the periplasm and transmits torque from the MS ring to the hook.
Subject
Predicate
Object
Evidence
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FliE, FlgB, FlgC and FlgF form the proximal rod and FlgG forms the distal rod. Together they make the central basal-body rod that spans the periplasm and transmits torque from the MS ring to the hook.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Flagellin protofilaments form a rotary propeller (FUNCTION)
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Flagellin subunits pack into protofilaments that form a long tubular helix. When the basal body transmits torque through the hook, rotation of that helical filament generates thrust for swimming motility.
Subject
Predicate
Object
Evidence
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Flagellin subunits pack into protofilaments that form a long tubular helix. When the basal body transmits torque through the hook, rotation of that helical filament generates thrust for swimming motility.
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Evidence
flagellin
polymerizes into
flagellin protofilament
DOI:10.1038/s41598-019-51440-1 Yonekura et al. 2019 resolved repeating flagellin subunits in an 11-protofilament Kurthia filament.
FliD caps the filament tip and guides flagellin addition (ASSEMBLY)
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FliD/HAP2 oligomerizes into a filament cap at the distal tip of the flagellar filament. The cap sits on the hook-filament junction before filament assembly and later moves at the filament end to guide exported flagellin subunits into the elongating lattice.
Subject
Predicate
Object
Evidence
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FliD/HAP2 oligomerizes into a filament cap at the distal tip of the flagellar filament. The cap sits on the hook-filament junction before filament assembly and later moves at the filament end to guide exported flagellin subunits into the elongating lattice.
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flagellar filament cap protein FliD/HAP2
oligomerizes into
bacterial-type flagellum filament cap
DOI:10.1006/jmbi.1996.0349 Ikeda et al. 1996 showed that FliD can self-assemble into annular cap-like structures.
FlgE builds the torque-transmitting hook (FUNCTION)
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FlgE subunits polymerize into a short curved tube. The resulting hook connects the basal body and filament, bends as the filament changes angle, and transmits motor torque into rotation of the filament propeller.
Subject
Predicate
Object
Evidence
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FlgE subunits polymerize into a short curved tube. The resulting hook connects the basal body and filament, bends as the filament changes angle, and transmits motor torque into rotation of the filament propeller.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Evidence
hook protein FlgE
polymerizes into
bacterial-type flagellum hook
DOI:10.1038/ncomms13425 Matsunami et al. 2016 resolved a complete Campylobacter jejuni hook built from polymerized FlgE.
hook protein FlgE
forms
FlgE intermolecular interfaces
DOI:10.3390/biom9090462 Horvath et al. 2019 modeled Salmonella FlgE intermolecular domain interactions in the hook.
FlgE intermolecular interfaces
stabilize
bacterial-type flagellum hook
DOI:10.1038/s41467-019-13252-9 Kato et al. 2019 linked the native supercoiled hook lattice to a flexible universal joint.
FlgK and FlgL connect the hook to the filament (FUNCTION)
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FlgK assembles next to the hook and FlgL next to the filament to form a two-layer hook-filament junction. The junction joins the flexible hook to the rigid filament, supports FliD cap placement during filament initiation, and buffers hook-derived mechanical stress.
Subject
Predicate
Object
Evidence
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FlgK assembles next to the hook and FlgL next to the filament to form a two-layer hook-filament junction. The junction joins the flexible hook to the rigid filament, supports FliD cap placement during filament initiation, and buffers hook-derived mechanical stress.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Dynamic stators anchor around the MS/C-ring rotor, ion flow through each stator applies torque to FliG in the C ring, the MS ring transmits rotation to the rod, and CheY-P shifts C-ring switching state.
Subject
Predicate
Object
Evidence
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Dynamic stators anchor around the MS/C-ring rotor, ion flow through each stator applies torque to FliG in the C ring, the MS ring transmits rotation to the rod, and CheY-P shifts C-ring switching state.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Evidence
bacterial-type flagellum stator complex
docks around
bacterial-type flagellum rotor complex
DOI:10.7554/eLife.48979 Chang et al. 2019 imaged stator complexes around bacterial flagellar rotors in cells.
MS and C rings form the flagellar rotor (FUNCTION)
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The C ring assembles on the MS ring, the C ring receives stator torque, the MS ring transmits rotation into the rod, and C-ring switching sets clockwise or counterclockwise output.
Subject
Predicate
Object
Evidence
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The C ring assembles on the MS ring, the C ring receives stator torque, the MS ring transmits rotation into the rod, and C-ring switching sets clockwise or counterclockwise output.
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bacterial-type flagellum basal body, MS ring
forms membrane-anchored ring in
bacterial-type flagellum rotor complex
DOI:10.1038/s41467-021-24507-9 Kawamoto et al. 2021 resolved the native Salmonella MS ring that anchors the rotor around the export gate.
bacterial-type flagellum basal body, C ring
forms cytoplasmic switch ring in
bacterial-type flagellum rotor complex
DOI:10.1038/emboj.2011.188 Paul et al. 2011 mapped the FliG/FliM/FliN subunits in the Salmonella rotor architecture.
bacterial-type flagellum basal body, MS ring
templates
bacterial-type flagellum basal body, C ring
DOI:10.1038/s41467-021-24507-9 Kawamoto et al. 2021 measured native Salmonella C-ring symmetry relative to the FliF MS ring.
FliP, FliQ and FliR form the small hydrophobic membrane core, FlhB caps that core, FlhA completes the membrane gate, FliH, FliI and FliJ assemble the cytoplasmic ATPase complex that couples to FlhA, and ATP plus ion motive force drive rod, hook and filament subunits through the MS-ring-embedded export apparatus.
Subject
Predicate
Object
Evidence
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FliP, FliQ and FliR form the small hydrophobic membrane core, FlhB caps that core, FlhA completes the membrane gate, FliH, FliI and FliJ assemble the cytoplasmic ATPase complex that couples to FlhA, and ATP plus ion motive force drive rod, hook and filament subunits through the MS-ring-embedded export apparatus.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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A-subunit pentamers and B-subunit dimers form ion-driven stators. B subunits anchor the complex to peptidoglycan, ion flow drives the A ring, and the stator applies torque to the C ring.
Subject
Predicate
Object
Evidence
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A-subunit pentamers and B-subunit dimers form ion-driven stators. B subunits anchor the complex to peptidoglycan, ion flow drives the A ring, and the stator applies torque to the C ring.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Ciliary transition zone gates the ciliary compartment (FUNCTION)
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Transition-zone Y-linkers and proteins organize a gate between axonemal microtubules and the ciliary membrane at the proximal cilium.
Subject
Predicate
Object
Evidence
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Transition-zone Y-linkers and proteins organize a gate between axonemal microtubules and the ciliary membrane at the proximal cilium.
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Evidence
transition-zone Y-linkers
connect
transition-zone axonemal microtubules
GO:0035869 GO:0035869 defines Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane.
transition-zone Y-linkers
tether to
ciliary membrane
DOI:10.1083/jcb.201006105 Craige et al. 2010 used Chlamydomonas cep290 mutants to link a transition-zone protein to normal microtubule-membrane connections.
ciliary transition zone
is part of
cilium
GO:0035869 GO relates the ciliary transition zone as part of the cilium.
Intraflagellar transport builds the ciliary axoneme (ASSEMBLY)
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A basal body seeds axoneme extension, a transition-zone gate organizes entry into the membrane-bounded ciliary compartment, and intraflagellar-transport particles move cargo along axonemal microtubules for cilium assembly.
Subject
Predicate
Object
Evidence
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A basal body seeds axoneme extension, a transition-zone gate organizes entry into the membrane-bounded ciliary compartment, and intraflagellar-transport particles move cargo along axonemal microtubules for cilium assembly.
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ciliary basal body
nucleates
axoneme
GO:0036064 GO:0036064 defines the ciliary basal body as the axoneme-growth nucleation site.
Csg secretion and nucleation build the curli fiber (ASSEMBLY)
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The outer-membrane CsgG pore and accessory factors move CsgA to the cell surface, CsgB nucleates CsgA polymerization, and the resulting amyloid polymer forms the curli fiber.
Subject
Predicate
Object
Evidence
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The outer-membrane CsgG pore and accessory factors move CsgA to the cell surface, CsgB nucleates CsgA polymerization, and the resulting amyloid polymer forms the curli fiber.
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Evidence
CsgG outer-membrane secretion pore
exports
CsgA major curlin subunit
DOI:10.1111/j.1365-2958.2005.04997.x Robinson et al. 2006 established the outer-membrane CsgG protein as the secretion route for curli fiber subunits.
CsgF cell-surface adaptor
positions
CsgB nucleator subunit
DOI:10.1073/pnas.0812143106 Nenninger et al. 2009 showed that CsgF is needed for localized, efficient curli nucleation by the CsgB pathway.
Proteinaceous hami present grappling hooks for surface adhesion (FUNCTION)
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The hami of Candidatus Altarchaeum hamiconexum contain 120 kDa subunits and present a helical filament with periodic prickles and a terminal grappling hook from the cell surface to mediate adhesion to biotic and abiotic surfaces.
Subject
Predicate
Object
Evidence
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The hami of Candidatus Altarchaeum hamiconexum contain 120 kDa subunits and present a helical filament with periodic prickles and a terminal grappling hook from the cell surface to mediate adhesion to biotic and abiotic surfaces.
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hamus 120 kDa subunits
are major constituents of
helical hamus filament
DOI:10.1111/j.1365-2958.2005.04294.x Moissl et al. 2005 characterized the dominant 120 kDa hamus subunits and the helical appendage ultrastructure.
Haptonemal microtubules support coiling and particle capture (FUNCTION)
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Singlet microtubules form the haptonemal core. Calcium-dependent microtubule conformational changes enable rapid coiling, and the protruding haptonema can attach to food particles during haptophyte feeding.
Subject
Predicate
Object
Evidence
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Singlet microtubules form the haptonemal core. Calcium-dependent microtubule conformational changes enable rapid coiling, and the protruding haptonema can attach to food particles during haptophyte feeding.
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haptonemal singlet microtubules
form core of
haptonema
DOI:10.1242/bio.036590 Nomura et al. 2019 describe prior ultrastructural observations of six to seven microtubules within the haptonema.
calcium-dependent conformational state
modulates
haptonemal singlet microtubules
DOI:10.1242/bio.036590 Nomura et al. 2019 found that a microtubule stabilizer blocked rapid haptonemal coiling without preventing Ca2+ influx.
haptonemal singlet microtubules
drive
rapid haptonemal coiling
DOI:10.1242/bio.036590 Nomura et al. 2019 linked rapid coiling to Ca2+-dependent conformational changes of haptonemal microtubules.
OmcE tetraheme c-type cytochromes polymerize into a helical extracellular filament whose packed hemes provide a candidate structural path for electron transfer.
Subject
Predicate
Object
Evidence
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OmcE tetraheme c-type cytochromes polymerize into a helical extracellular filament whose packed hemes provide a candidate structural path for electron transfer.
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OmcE tetraheme c-type cytochrome
polymerizes into
OmcE cytochrome nanowire
DOI:10.1038/s41564-022-01159-z Wang et al. 2022 determined the cryo-EM structure of a Geobacter OmcE cytochrome filament assembled from OmcE tetraheme cytochromes.
OmcS monomers align hemes for nanowire conduction (FUNCTION)
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OmcS six-heme c-type cytochrome monomers polymerize into a helical extracellular filament in which a stacked heme chain runs along the nanowire axis and provides a path for long-range electron transfer.
Subject
Predicate
Object
Evidence
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OmcS six-heme c-type cytochrome monomers polymerize into a helical extracellular filament in which a stacked heme chain runs along the nanowire axis and provides a path for long-range electron transfer.
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OmcS six-heme c-type cytochrome
polymerizes into
OmcS cytochrome nanowire
DOI:10.1038/s42003-019-0448-9 Filman et al. 2019 reconstructed OmcS monomers stacked head-to-tail in a helical bacterial nanowire.
OmcS six-heme c-type cytochrome
aligns
stacked heme chain
DOI:10.1016/j.cell.2019.03.029 Wang et al. 2019 described the stacked heme arrangement in the OmcS filament cryo-EM structure.
DOI:10.1038/s42003-019-0448-9 Filman et al. 2019 resolved OmcS monomers around an unbranched heme chain in the filament core.
stacked heme chain
supports
long-range extracellular electron transfer
DOI:10.1016/j.cell.2019.03.029 Wang et al. 2019 linked heme packing to electron transport over micrometer-length OmcS nanowires.
DOI:10.1038/s42003-019-0448-9 Filman et al. 2019 proposed the heme chain as the filament's long-range electron transport path.
OmcZ subunits branch hemes for nanowire conduction (FUNCTION)
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OmcZ octaheme c-type cytochromes polymerize into an extracellular filament whose branched heme arrangement and surface-exposed heme site provide a candidate structural basis for conductive OmcZ nanowires.
Subject
Predicate
Object
Evidence
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OmcZ octaheme c-type cytochromes polymerize into an extracellular filament whose branched heme arrangement and surface-exposed heme site provide a candidate structural basis for conductive OmcZ nanowires.
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OmcZ octaheme c-type cytochrome
polymerizes into
OmcZ cytochrome nanowire
DOI:10.7554/eLife.81551 Wang et al. 2022 determined a cryo-EM structure of Geobacter sulfurreducens OmcZ filaments formed from the OmcZ octaheme cytochrome.
OmcZ octaheme c-type cytochrome
arranges
branched heme network
DOI:10.7554/eLife.81551 Wang et al. 2022 reported that OmcZ heme packing and between-subunit coordination differ from the linear OmcS and OmcE heme chains.
branched heme network
exposes
surface-exposed heme site
DOI:10.7554/eLife.81551 Wang et al. 2022 proposed that the surface-exposed heme in each OmcZ subunit may help explain conductive biofilm network formation.
PapC assembles the PapD-delivered P pilus tip and rod (ASSEMBLY)
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PapD carries pilus subunits to the PapC usher. PapC initiates assembly with the distal PapG adhesin, then incorporates PapF and PapE to build the tip fibrillum, PapK to bridge the tip to the rod, PapA repeatedly to form the rod, and PapH to terminate and anchor the completed appendage.
Subject
Predicate
Object
Evidence
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PapD carries pilus subunits to the PapC usher. PapC initiates assembly with the distal PapG adhesin, then incorporates PapF and PapE to build the tip fibrillum, PapK to bridge the tip to the rod, PapA repeatedly to form the rod, and PapH to terminate and anchor the completed appendage.
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PapD chaperone
delivers to
PapC usher
DOI:10.1128/ecosalplus.ESP-0007-2017 Werneburg and Thanassi 2018 review the PapD periplasmic chaperone and PapC usher steps of P pilus biogenesis.
PFR1 and PFR2 build the paraflagellar rod lattice (ASSEMBLY)
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PFR1 and PFR2 are transported into the flagellum and co-assemble into the extra-axonemal paraflagellar rod lattice. Cytoplasmic PFR-AF1 and PFR-AF2 act before flagellar entry and are needed to accumulate the major PFR proteins and form the mature rod.
Subject
Predicate
Object
Evidence
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PFR1 and PFR2 are transported into the flagellum and co-assemble into the extra-axonemal paraflagellar rod lattice. Cytoplasmic PFR-AF1 and PFR-AF2 act before flagellar entry and are needed to accumulate the major PFR proteins and form the mature rod.
+Directed graph · arrows run from subject to object. Focus or hover over a node or arrow for details; the evidence table follows.
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Object
Evidence
69 kDa paraflagellar rod protein PFR1
co-assembles into
paraflagellar rod
DOI:10.1128/MCB.19.12.8191 Bastin et al. 1999 tracked tagged PFRA/PFR1 addition to new and old T. brucei PFRs.
73 kDa paraflagellar rod protein PFR2
co-assembles into
paraflagellar rod
DOI:10.1242/jcs.112.16.2753 Maga et al. 1999 showed that Leishmania PFR filaments contain PFR1 and PFR2 and that PFR2 mutants fail to assemble a native PFR.
paraflagellar rod
anchors to
axoneme
DOI:10.1242/jcs.112.16.2753 Maga et al. 1999 used Leishmania PFR mutants to show that fibers attaching the PFR to the axoneme can assemble in the absence of the bulk PFR.
A sheathed FlaB filament rotates in the periplasm to deform the cell cylinder (FUNCTION)
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FlaB proteins form the core of a sheathed periplasmic filament, the polar basal body anchors and drives rotation of that filament, and internal flagellar rotation changes spirochete cell shape to generate motility.
Subject
Predicate
Object
Evidence
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FlaB proteins form the core of a sheathed periplasmic filament, the polar basal body anchors and drives rotation of that filament, and internal flagellar rotation changes spirochete cell shape to generate motility.
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Evidence
FlaB core flagellins
polymerizes into
sheathed periplasmic flagellar filament
DOI:10.3390/biom10040550 Nakamura 2020 reviews the conserved FlaB core of spirochete periplasmic flagellar filaments.
FlaA sheath proteins
forms sheath around
sheathed periplasmic flagellar filament
DOI:10.1016/j.tim.2022.09.010 San Martin et al. 2023 review the FlaA sheath surrounding polymerized FlaB protomers in the spirochete periplasmic flagellar filament.
sheathed periplasmic flagellar filament
is part of
periplasmic flagellum
DOI:10.1371/journal.pbio.3000050 Qin et al. 2018 resolved filaments connected to polar periplasmic flagellar motors in Borrelia burgdorferi.
Nonhomologous pilus structural subunits polymerize into surface-exposed protein fibers that let bacterial cells interact with surfaces, host cells, neighboring cells or extracellular DNA.
Subject
Predicate
Object
Evidence
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Nonhomologous pilus structural subunits polymerize into surface-exposed protein fibers that let bacterial cells interact with surfaces, host cells, neighboring cells or extracellular DNA.
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pilus structural subunits
polymerize into
pilus
uniprot.location:SL-0113 UniProt Subcellular Location entry SL-0113 describes the fimbrium/pilus class as polymeric filamentous appendages.
pilus
supports
bacterial surface interaction
uniprot.location:SL-0113 UniProt Subcellular Location entry SL-0113 describes adhesion, motility, cell-cell interaction, biofilm, conjugation and DNA uptake roles for pili.
MreB-dependent wall synthesis extends the Caulobacter stalk (ASSEMBLY)
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Cell-cycle regulators control Caulobacter stalk biogenesis, MreB-dependent stalk-wall machinery builds stalk-specific peptidoglycan, and continued envelope extension yields a polar prostheca whose StpX and crossband proteins help maintain local stalk organization.
Subject
Predicate
Object
Evidence
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Cell-cycle regulators control Caulobacter stalk biogenesis, MreB-dependent stalk-wall machinery builds stalk-specific peptidoglycan, and continued envelope extension yields a polar prostheca whose StpX and crossband proteins help maintain local stalk organization.
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CpaF extends and retracts PilA Tad pili (FUNCTION)
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PilA subunits polymerize into a polar Tad pilus filament, the CpaF motor drives filament extension and retraction, and retraction after surface contact keeps the cell near abiotic surfaces during early colonization.
Subject
Predicate
Object
Evidence
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PilA subunits polymerize into a polar Tad pilus filament, the CpaF motor drives filament extension and retraction, and retraction after surface contact keeps the cell near abiotic surfaces during early colonization.
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Object
Evidence
PilA major pilin
polymerizes into
Tad pilus
DOI:10.1128/mBio.01237-19 Sangermani et al. 2019 track dynamic Caulobacter Tad pili built from PilA pilin.
CpaF Tad pilus motor
extends and retracts
Tad pilus
DOI:10.1038/s41467-024-50280-6 Hohl et al. 2024 structurally and biochemically analyze bidirectional pilus processing by CpaF.
DOI:10.1126/science.aan5706 Ellison et al. 2017 show that Caulobacter Tad pili retract and that retraction obstruction stimulates surface sensing.
Tad pilus
contacts
abiotic surface
DOI:10.1128/mBio.01237-19 Sangermani et al. 2019 image Tad pilus extension toward the surface during Caulobacter colonization assays.
FimC and FimD polymerize the type I pilus tip and rod (ASSEMBLY)
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FimC carries folded pilus subunits to the outer-membrane FimD usher. FimD accepts the FimH adhesin, FimG adaptor, and FimF adaptor before adding FimA repeatedly into the helical rod, then the FimI terminator caps the basal end and anchors the rod at the usher.
Subject
Predicate
Object
Evidence
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FimC carries folded pilus subunits to the outer-membrane FimD usher. FimD accepts the FimH adhesin, FimG adaptor, and FimF adaptor before adding FimA repeatedly into the helical rod, then the FimI terminator caps the basal end and anchors the rod at the usher.
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Evidence
FimC chaperone
delivers to
FimD usher
DOI:10.1128/ecosalplus.ESP-0007-2017 Werneburg and Thanassi 2018 review the FimC periplasmic chaperone and FimD outer-membrane usher steps of type 1 pilus biogenesis.
FimD usher
assembles tip from
FimH tip adhesin
DOI:10.1128/ecosalplus.ESP-0007-2017 Werneburg and Thanassi 2018 describe ordered chaperone-usher incorporation of the type 1 pilus tip subunits.
FimH tip adhesin
connects to
FimG tip adaptor subunit
DOI:10.1038/s41467-025-60325-z Bachmann et al. 2025 structurally model FimG immediately proximal to FimH in the type 1 pilus tip.
PilB and PilT drive type IV pilus extension-retraction cycles (FUNCTION)
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The extension ATPase assembles pilin subunits into the extracellular filament, and the retraction ATPase pulls an attached filament back through the envelope. Surface-attached retraction generates the force used for twitching motility.
Subject
Predicate
Object
Evidence
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The extension ATPase assembles pilin subunits into the extracellular filament, and the retraction ATPase pulls an attached filament back through the envelope. Surface-attached retraction generates the force used for twitching motility.
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Evidence
PilB-family extension ATPase
extends
type IV pilus
DOI:10.1038/nrmicro.2017.40 Hospenthal, Costa and Waksman 2017 review the PilB-family ATPase as the motor that extends Gram-negative type IV pili.
major type IV pilin
polymerizes into
type IV pilus
DOI:10.1038/nrmicro.2017.40 Hospenthal, Costa and Waksman 2017 describe T4P fibres as polymers of pilin subunits assembled by the biogenesis machinery.
type IV pilus
reaches
surface-bound type IV pilus
DOI:10.1073/pnas.121171698 Skerker and Berg 2001 directly observed Pseudomonas aeruginosa type IV pili extending, attaching at their distal ends and retracting.
Arp2/3 nucleates a branched actin network in yeast cortical patches (ASSEMBLY)
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In Saccharomyces cerevisiae, Arp2/3 promotes formation of short branched actin filaments at cortical endocytic sites, producing actin cortical patches.
Subject
Predicate
Object
Evidence
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In Saccharomyces cerevisiae, Arp2/3 promotes formation of short branched actin filaments at cortical endocytic sites, producing actin cortical patches.
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Evidence
Arp2/3 protein complex
nucleates branches in
actin cortical patch
DOI:10.1083/jcb.200404159 Young, Cooper and Bridgman 2004 linked the patch branch pattern to Arp2/3-mediated actin polymerization.
actin
polymerizes into
actin cortical patch
DOI:10.1083/jcb.200404159 Young, Cooper and Bridgman 2004 found networks of branched actin filaments in yeast actin patches.
Dynein and regulatory complexes bend Chlamydomonas axonemes (FUNCTION)
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In Chlamydomonas, dynein arms connect outer doublet microtubules to generate sliding forces; radial spokes, central-pair structures, and nexin-dynein regulatory links organize and coordinate the 9+2 flagellar axoneme.
Subject
Predicate
Object
Evidence
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In Chlamydomonas, dynein arms connect outer doublet microtubules to generate sliding forces; radial spokes, central-pair structures, and nexin-dynein regulatory links organize and coordinate the 9+2 flagellar axoneme.
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Evidence
outer doublet microtubules
form scaffold of
axoneme
DOI:10.1126/science.1128618 Nicastro et al. 2006 resolved the outer doublet microtubules of the Chlamydomonas axoneme by cryoelectron tomography.
axonemal dynein arms
bridge
outer doublet microtubules
DOI:10.1126/science.1128618 Nicastro et al. 2006 visualized dynein-microtubule organization in 9+2 axonemes.
radial spokes
project toward
central pair apparatus
DOI:10.1126/science.1128618 Nicastro et al. 2006 identified radial spokes and the central-pair region in the Chlamydomonas axoneme.
Bilobe protein cohorts flank pocket-associated cytoskeleton (FUNCTION)
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TbMORN1 and bilobe centrins mark the hooked and hairpin regions of the T. brucei bilobe, which sits between the flagellar pocket collar and the flagellum attachment zone-associated microtubule quartet.
Subject
Predicate
Object
Evidence
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TbMORN1 and bilobe centrins mark the hooked and hairpin regions of the T. brucei bilobe, which sits between the flagellar pocket collar and the flagellum attachment zone-associated microtubule quartet.
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BtubA/B subunits form a bacterial microtubule (ASSEMBLY)
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BtubA and BtubB co-assemble into tubulin-like microtubules, and BtubC binds the BtubAB polymer exterior as stabilizing associated machinery.
Subject
Predicate
Object
Evidence
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BtubA and BtubB co-assemble into tubulin-like microtubules, and BtubC binds the BtubAB polymer exterior as stabilizing associated machinery.
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BtubA
co-assembles into
BtubAB bacterial microtubule
DOI:10.1371/journal.pbio.1001213 Pilhofer et al. 2011 assigned BtubA/B proteins to tube-like structures in Prosthecobacter and reconstituted bacterial microtubule-like tubes.
DOI:10.1073/pnas.1705062114 Deng et al. 2017 resolved alternating BtubA and BtubB subunits in a purified mini-microtubule.
BtubB
co-assembles into
BtubAB bacterial microtubule
DOI:10.1371/journal.pbio.1001213 Pilhofer et al. 2011 assigned BtubA/B proteins to tube-like structures in Prosthecobacter and reconstituted bacterial microtubule-like tubes.
DOI:10.1073/pnas.1705062114 Deng et al. 2017 resolved alternating BtubA and BtubB subunits in a purified mini-microtubule.
CetZ filaments support Haloferax rod-cell development (FUNCTION)
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CetZ1-like proteins polymerize into envelope-associated dynamic filaments that remodel the Haloferax volcanii envelope and promote rod-shape development.
Subject
Predicate
Object
Evidence
+
CetZ1-like proteins polymerize into envelope-associated dynamic filaments that remodel the Haloferax volcanii envelope and promote rod-shape development.
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CetZ1-like proteins
polymerize into
CetZ filament
DOI:10.1038/nature13983 Duggin et al. 2015 resolved CetZ protofilament-like crystal packing and observed dynamic CetZ1-GFP filaments in Haloferax cells.
CetZ filament
associates with
archaeal cell envelope
DOI:10.1038/nature13983 Duggin et al. 2015 localized CetZ1-GFP spots and short filaments at or near the cell envelope.
CetZ filament
supports
Haloferax rod cell development
DOI:10.1038/nature13983 Duggin et al. 2015 connected CetZ1 structures with envelope remodeling and rod-cell development.
The cartwheel organizes the triplet microtubule cylinder (ASSEMBLY)
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A proximal cartwheel organizes ninefold basal-body symmetry, nine triplet microtubule blades form the basal-body cylinder, and the assembled basal body anchors the cilium and nucleates axonemal microtubules.
Subject
Predicate
Object
Evidence
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A proximal cartwheel organizes ninefold basal-body symmetry, nine triplet microtubule blades form the basal-body cylinder, and the assembled basal body anchors the cilium and nucleates axonemal microtubules.
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basal-body cartwheel
organizes
basal-body triplet microtubules
DOI:10.1083/jcb.200402022 Matsuura et al. 2004 localized Bld10p to the cartwheel and proposed that it acts early in Chlamydomonas basal-body assembly.
basal-body triplet microtubules
form wall of
ciliary basal body
DOI:10.1186/s13630-016-0039-z Dutcher and O'Toole 2016 review the nine triplet microtubules of Chlamydomonas basal bodies.
ciliary basal body
nucleates
axoneme
GO:0036064 GO defines the ciliary basal body as a ciliary base structure that nucleates axoneme growth.
BILBO1 polymers recruit partner proteins at the FPC (ASSEMBLY)
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BILBO1 dimerizes and polymerizes into a scaffold at the flagellar pocket collar. FPC4 binds the BILBO1 N-terminal domain and microtubules, while BILBO2 adds a second BILBO-family FPC component that shares the FPC4 binding interface.
Subject
Predicate
Object
Evidence
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BILBO1 dimerizes and polymerizes into a scaffold at the flagellar pocket collar. FPC4 binds the BILBO1 N-terminal domain and microtubules, while BILBO2 adds a second BILBO-family FPC component that shares the FPC4 binding interface.
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BILBO1
dimerizes into
BILBO1 antiparallel dimer
DOI:10.1074/jbc.M114.554659 Vidilaseris et al. 2014 dissected BILBO1 domains and linked the coiled coil and leucine zipper to dimerization and filament formation.
BILBO1 antiparallel dimer
polymerizes into
BILBO1 polymer
DOI:10.1074/jbc.M114.554659 Vidilaseris et al. 2014 connected BILBO1 leucine-zipper interdimer interactions with extended in-vitro filament assembly.
BILBO1 polymer
scaffolds
ciliary pocket collar
DOI:10.1371/journal.ppat.1004654 Florimond et al. 2015 showed that BILBO1 has intrinsic polymer-forming properties and that its coiled-coil domain targets BILBO1 to the FPC.
Tubulin conoid fibers and MyoH support parasite entry and exit (FUNCTION)
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Tubulin protofilament ribbons form the spiral conoid at the apical complex, where conoid-complex proteins and the MyoH motor support Toxoplasma entry into and exit from host cells.
Subject
Predicate
Object
Evidence
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Tubulin protofilament ribbons form the spiral conoid at the apical complex, where conoid-complex proteins and the MyoH motor support Toxoplasma entry into and exit from host cells.
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Caulobacter CtpS polymerizes into an inner-curvature filament that functionally interacts with crescentin and supports curved cell morphology.
Subject
Predicate
Object
Evidence
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Caulobacter CtpS polymerizes into an inner-curvature filament that functionally interacts with crescentin and supports curved cell morphology.
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CTP synthase
polymerizes into
cytoophidium
DOI:10.1038/ncb2087 Ingerson-Mahar et al. 2010 used fluorescence microscopy and electron cryo-tomography to identify CtpS as the Caulobacter inner-curvature filament protein.
cytoophidium
localizes to
Caulobacter inner cell curvature
DOI:10.1038/ncb2087 Ingerson-Mahar et al. 2010 followed mCherry-CtpS structures that elongated and moved to the inner cell curvature.
cytoophidium
functionally interacts with
crescentin filament
DOI:10.1038/ncb2087 Ingerson-Mahar et al. 2010 connected the CtpS morphogenic role to a functional interaction with crescentin.
Pil1 and Lsp1 assemble into a cytoplasmic eisosome filament that scaffolds the paired MCC plasma-membrane domain.
Subject
Predicate
Object
Evidence
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Pil1 and Lsp1 assemble into a cytoplasmic eisosome filament that scaffolds the paired MCC plasma-membrane domain.
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Pil1/Lsp1 BAR-domain eisosome core
assembles into
eisosome filament
DOI:10.1091/mbc.e10-12-1021 Olivera-Couto et al. 2011 established Pil1 and Lsp1 as the BAR-domain core components of Saccharomyces cerevisiae eisosomes.
eisosome filament
scaffolds
eisosome membrane domain/MCC
DOI:10.1083/jcb.201104040 Karotki et al. 2011 showed that purified Pil1 and Lsp1 assemble into eisosome-like membrane scaffolds.
FAZ filament proteins maintain lateral flagellum attachment (FUNCTION)
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FAZ1, FAZ2 and CC2D are curated T. brucei FAZ filament constituents that contribute to the FAZ cytoskeletal filament; the larger FAZ network mediates lateral flagellum attachment and helps set trypanosome morphology.
Subject
Predicate
Object
Evidence
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FAZ1, FAZ2 and CC2D are curated T. brucei FAZ filament constituents that contribute to the FAZ cytoskeletal filament; the larger FAZ network mediates lateral flagellum attachment and helps set trypanosome morphology.
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MamK filaments organize magnetosome chains (FUNCTION)
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MamK proteins polymerize into cytoskeletal filaments that run along magnetosome chains and help maintain the organelles in a linear arrangement.
Subject
Predicate
Object
Evidence
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MamK proteins polymerize into cytoskeletal filaments that run along magnetosome chains and help maintain the organelles in a linear arrangement.
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MamK actin homolog
polymerizes into
MamK filament
DOI:10.1002/pro.2979 Bergeron et al. 2017 solved the polymerized MamK filament by cryo-EM.
MamK filament
organizes
magnetosome
DOI:10.1126/science.1123231 Komeili et al. 2006 used electron cryotomography to connect cytoskeletal filaments and MamK with magnetosome organization in AMB-1 cells.
MamK filament
aligns
magnetosome chain
DOI:10.1038/nrmicro.2016.99 Uebe and Schuler 2016 describe MamK/MamJ-dependent magnetosome chain organization.
MreB and RodZ orient sidewall synthesis to preserve a rod (FUNCTION)
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MreB subunits form membrane-associated filaments that RodZ couples to the elongasome. Those filaments orient circumferential sidewall peptidoglycan synthesis, and the resulting feedback keeps rod-shaped cells from widening into spheres.
Subject
Predicate
Object
Evidence
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MreB subunits form membrane-associated filaments that RodZ couples to the elongasome. Those filaments orient circumferential sidewall peptidoglycan synthesis, and the resulting feedback keeps rod-shaped cells from widening into spheres.
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MreB
polymerizes into
MreB filament
DOI:10.1016/j.cell.2018.02.050 Shi, Bratton, Gitai and Huang 2018 review E. coli MreB filament architecture and membrane association.
RodZ
couples
elongasome
DOI:10.1016/j.cell.2018.02.050 Shi, Bratton, Gitai and Huang 2018 review cytoplasmic RodZ-MreB binding and periplasmic RodZ contacts with wall-synthesis enzymes.
MreB filament
orients
elongasome
DOI:10.1016/j.cell.2018.02.050 Shi, Bratton, Gitai and Huang 2018 describe MreB as a curvature sensor that both detects and changes local shape.
ParM polymerizes into actin-like filaments that are captured by ParR-parC complexes on R1 plasmids; stabilized filament elongation supports plasmid segregation.
Subject
Predicate
Object
Evidence
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ParM polymerizes into actin-like filaments that are captured by ParR-parC complexes on R1 plasmids; stabilized filament elongation supports plasmid segregation.
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ParM
polymerizes into
ParM filament
DOI:10.1093/emboj/cdf320 Moller-Jensen et al. 2002 observed R1 ParM filaments in bacterial cells.
PhuZ spindles position jumbo-phage nuclei (FUNCTION)
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Phage-encoded PhuZ polymerizes into dynamic filaments of a bipolar spindle that positions the jumbo-phage nucleus in infected bacterial cells.
Subject
Predicate
Object
Evidence
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Phage-encoded PhuZ polymerizes into dynamic filaments of a bipolar spindle that positions the jumbo-phage nucleus in infected bacterial cells.
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PhuZ
polymerizes into
PhuZ spindle
DOI:10.7554/eLife.03197 Erb et al. 2014 characterized PhuZ dynamic polymerization during 201phi2-1 infection.
DOI:10.1016/j.celrep.2017.07.064 Chaikeeratisak et al. 2017 observed PhuZ polymers forming bipolar spindle structures in infected cells.
PhuZ spindle
positions
phage nucleus
DOI:10.1016/j.celrep.2017.07.064 Chaikeeratisak et al. 2017 linked PhuZ spindles with positioning of phage nucleus-like compartments in large Pseudomonas phages.
PhuZ spindle
supports
phage nucleus positioning
DOI:10.7554/eLife.03197 Erb et al. 2014 connected PhuZ dynamic instability with centering of phage DNA in infected cells.
APR2 maintains the APR gate for F-actin flux, motility, and invasion (FUNCTION)
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APR proteins occupy layered positions in the Toxoplasma apical polar ring; APR2 in the upper layer maintains APR integrity, supports conoid extrusion, and helps route F-actin through the pellicular space to sustain gliding motility and host-cell invasion.
Subject
Predicate
Object
Evidence
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APR proteins occupy layered positions in the Toxoplasma apical polar ring; APR2 in the upper layer maintains APR integrity, supports conoid extrusion, and helps route F-actin through the pellicular space to sustain gliding motility and host-cell invasion.
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APR2-to-APR7 apical polar ring proteins
localize to
polar ring of apical complex
DOI:10.1073/pnas.2416602121 Ren et al. 2024 used ultrastructure expansion microscopy to assign APR proteins to upper, middle, and bottom APR layers.
APR2 upper-layer protein
localizes to
upper APR layer
DOI:10.1073/pnas.2416602121 Ren et al. 2024 identified APR2 as a key structural component of the upper APR layer.
Budding-yeast septin hetero-octamers polymerize into a cortical ring (ASSEMBLY)
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In Saccharomyces cerevisiae, septin proteins assemble into hetero-octameric rods, the rods polymerize into septin filaments, and septin filaments organize at the bud-neck cortex to form the septin ring.
Subject
Predicate
Object
Evidence
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In Saccharomyces cerevisiae, septin proteins assemble into hetero-octameric rods, the rods polymerize into septin filaments, and septin filaments organize at the bud-neck cortex to form the septin ring.
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septin proteins
oligomerize into
budding-yeast septin hetero-octamer
DOI:10.1073/pnas.0803330105 Bertin et al. 2008 reconstituted Saccharomyces cerevisiae septin hetero-octamers and studied their supramolecular assembly.
budding-yeast septin hetero-octamer
polymerizes into
septin filaments
DOI:10.1073/pnas.0803330105 Bertin et al. 2008 visualized purified budding-yeast septin hetero-octamers polymerizing into filaments.
TAC domains bridge basal bodies to the kDNA disk (FUNCTION)
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The tripartite attachment complex is organized as unilateral filaments, specialized mitochondrial membranes and exclusion-zone filaments that span from the flagellar basal body side of the cell to the kinetoplast DNA disk.
Subject
Predicate
Object
Evidence
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The tripartite attachment complex is organized as unilateral filaments, specialized mitochondrial membranes and exclusion-zone filaments that span from the flagellar basal body side of the cell to the kinetoplast DNA disk.
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ciliary basal body
aligns with
unilateral filaments
DOI:10.1091/mbc.E02-08-0525 Ogbadoyi, Robinson and Gull 2003 placed unilateral filaments on the basal-body-facing side of the TAC.
unilateral filaments
connect through
differentiated mitochondrial TAC membrane regions
DOI:10.1091/mbc.E02-08-0525 Ogbadoyi, Robinson and Gull 2003 resolved a tripartite linkage with cytoplasmic filaments, differentiated mitochondrial membranes and matrix-side filaments.
differentiated mitochondrial TAC membrane regions
connect to
exclusion-zone filaments
DOI:10.1091/mbc.E02-08-0525 Ogbadoyi, Robinson and Gull 2003 resolved exclusion-zone filaments on the kinetoplast side of the differentiated membrane domain.
The Giardia ventral disc is built on a spiral microtubule scaffold with microribbons, crossbridges and a lateral crest; this domed cytoskeletal architecture supports trophozoite attachment to host epithelium.
Subject
Predicate
Object
Evidence
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The Giardia ventral disc is built on a spiral microtubule scaffold with microribbons, crossbridges and a lateral crest; this domed cytoskeletal architecture supports trophozoite attachment to host epithelium.
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ventral disc tubulins
polymerize into
ventral disc microtubule array
DOI:10.1371/journal.pone.0043783 Schwartz et al. 2012 resolved the Giardia ventral disc microtubule spiral by electron tomography.
ventral disc microtubule array
forms scaffold of
ventral disc
GO:0097593 Gene Ontology models GO:0097593 as the ventral disc microtubule-array substructure.
DOI:10.1371/journal.pone.0043783 Schwartz et al. 2012 resolved the Giardia ventral disc microtubule spiral by electron tomography.