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- PDB-9nw3: Ciliary tip central pair -

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Basic information

Entry
Database: PDB / ID: 9nw3
TitleCiliary tip central pair
Components
  • C2 domain protein
  • CFAP213
  • Cation channel family protein
  • Dpy-30 motif protein
  • Sperm flagellar protein
  • TLP1
  • TLP2
  • Tubulin alpha chain
  • Tubulin beta chain
  • Unknown
KeywordsPROTEIN BINDING / cilia / microtubules / central pair
Function / homology
Function and homology information


actomyosin structure organization / motile cilium / regulation of cytoskeleton organization / axoneme / microtubule-based process / structural constituent of cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton ...actomyosin structure organization / motile cilium / regulation of cytoskeleton organization / axoneme / microtubule-based process / structural constituent of cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / hydrolase activity / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
LSDAT, prokaryote / SLOG in TRPM, prokaryote / : / CH-like domain in sperm protein / CH-like domain in sperm protein / : / Dpy-30 motif / Dpy-30 motif / Calponin homology domain / CH domain superfamily ...LSDAT, prokaryote / SLOG in TRPM, prokaryote / : / CH-like domain in sperm protein / CH-like domain in sperm protein / : / Dpy-30 motif / Dpy-30 motif / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / C2 domain / C2 domain / C2 domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / C2 domain superfamily / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Tubulin alpha chain / Tubulin beta chain / Sperm flagellar protein / Dpy-30 motif protein / C2 domain protein / Cation channel family protein
Similarity search - Component
Biological speciesTetrahymena thermophila CU428 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLegal, T.L. / Bui, K.H.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-156354 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04774 Canada
CitationJournal: Curr Biol / Year: 2025
Title: Structure of the ciliary tip central pair reveals the unique role of the microtubule-seam binding protein SPEF1.
Authors: Thibault Legal / Ewa Joachimiak / Mireya Parra / Wang Peng / Amanda Tam / Corbin Black / Mayukh Guha / Chau Anh Nguyen / Avrin Ghanaeian / Melissa Valente-Paterno / Gary Brouhard / Jacek ...Authors: Thibault Legal / Ewa Joachimiak / Mireya Parra / Wang Peng / Amanda Tam / Corbin Black / Mayukh Guha / Chau Anh Nguyen / Avrin Ghanaeian / Melissa Valente-Paterno / Gary Brouhard / Jacek Gaertig / Dorota Wloga / Khanh Huy Bui /
Abstract: Motile cilia are unique organelles with the ability to move autonomously. The force generated by beating cilia propels cells and moves fluids. The ciliary skeleton is made of peripheral doublet ...Motile cilia are unique organelles with the ability to move autonomously. The force generated by beating cilia propels cells and moves fluids. The ciliary skeleton is made of peripheral doublet microtubules and a central pair (CP) with a distinct structure at the tip. In this study, we present a high-resolution structure of the CP in the ciliary tip of the ciliate Tetrahymena thermophila and identify several tip proteins that bind and form unique patterns on both microtubules of the tip CP. Two of those proteins that contain tubulin polymerization-promoting protein (TPPP)-like domains, TLP1 and TLP2, bind to high curvature regions of the microtubule. TLP2, which contains two TPPP-like domains, is an unusually long protein that wraps laterally around half a microtubule and forms the bridge between the two microtubules. Moreover, we found that the conserved protein SPEF1 binds to both microtubule seams and crosslinked the two microtubules. In vitro, human SPEF1 binds to the microtubule seam as visualized by cryoelectron tomography and subtomogram averaging. Single-molecule microtubule dynamics assays indicate that SPEF1 stabilizes microtubules in vitro. Together, these data show that the proteins in the tip CP maintain stable microtubule structures and play important roles in maintaining the integrity of the axoneme.
History
DepositionMar 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Tubulin alpha chain
AB: Tubulin beta chain
AC: Tubulin alpha chain
AD: Tubulin beta chain
AE: Tubulin alpha chain
AF: Tubulin beta chain
BA: Tubulin alpha chain
BB: Tubulin beta chain
BC: Tubulin alpha chain
BD: Tubulin beta chain
BE: Tubulin alpha chain
BF: Tubulin beta chain
CA: Tubulin alpha chain
CB: Tubulin beta chain
CC: Tubulin alpha chain
CD: Tubulin beta chain
CE: Tubulin alpha chain
CF: Tubulin beta chain
DA: Tubulin alpha chain
DB: Tubulin beta chain
DC: Tubulin alpha chain
DD: Tubulin beta chain
DE: Tubulin alpha chain
DF: Tubulin beta chain
EA: Tubulin alpha chain
EB: Tubulin beta chain
EC: Tubulin alpha chain
ED: Tubulin beta chain
EE: Tubulin alpha chain
EF: Tubulin beta chain
FA: Tubulin alpha chain
FB: Tubulin beta chain
FC: Tubulin alpha chain
FD: Tubulin beta chain
FE: Tubulin alpha chain
FF: Tubulin beta chain
GA: Tubulin alpha chain
GB: Tubulin beta chain
GC: Tubulin alpha chain
GD: Tubulin beta chain
GE: Tubulin alpha chain
GF: Tubulin beta chain
HA: Tubulin alpha chain
HB: Tubulin beta chain
HC: Tubulin alpha chain
HD: Tubulin beta chain
HE: Tubulin alpha chain
HF: Tubulin beta chain
IA: Tubulin alpha chain
IB: Tubulin beta chain
IC: Tubulin alpha chain
ID: Tubulin beta chain
IE: Tubulin alpha chain
IF: Tubulin beta chain
JA: Tubulin alpha chain
JB: Tubulin beta chain
JC: Tubulin alpha chain
JD: Tubulin beta chain
JE: Tubulin alpha chain
JF: Tubulin beta chain
KA: Tubulin alpha chain
KB: Tubulin beta chain
KC: Tubulin alpha chain
KD: Tubulin beta chain
KE: Tubulin alpha chain
KF: Tubulin beta chain
LA: Tubulin alpha chain
LB: Tubulin beta chain
LC: Tubulin alpha chain
LD: Tubulin beta chain
LE: Tubulin alpha chain
LF: Tubulin beta chain
MA: Tubulin alpha chain
MB: Tubulin beta chain
MC: Tubulin alpha chain
MD: Tubulin beta chain
ME: Tubulin alpha chain
MF: Tubulin beta chain
1A: Sperm flagellar protein
1B: Sperm flagellar protein
1C: Sperm flagellar protein
2A: TLP1
2B: TLP1
2C: TLP1
3A: C2 domain protein
3B: C2 domain protein
3C: C2 domain protein
4A: CFAP213
4B: CFAP213
4C: CFAP213
4D: CFAP213
5A: TLP2
5B: TLP2
5C: TLP2
6A: Cation channel family protein
6B: Cation channel family protein
6C: Cation channel family protein
7A: Dpy-30 motif protein
7B: Dpy-30 motif protein
7C: Dpy-30 motif protein
7D: Dpy-30 motif protein
7E: Dpy-30 motif protein
7F: Dpy-30 motif protein
8A: Unknown
8B: Unknown
8C: Unknown
8D: Unknown
8E: Unknown
8F: Unknown
8G: Unknown
8H: Unknown
8I: Unknown
8J: Unknown
8K: Unknown
8L: Unknown
8M: Unknown
8N: Unknown
8O: Unknown
8P: Unknown
8Q: Unknown
8R: Unknown
8S: Unknown
8T: Unknown
8U: Unknown
8V: Unknown
8W: Unknown
8X: Unknown
8Y: Unknown
8Z: Unknown
9A: Unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,463,827247
Polymers5,425,191130
Non-polymers38,637117
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 9 types, 103 molecules AAACAEBABCBECACCCEDADCDEEAECEEFAFCFEGAGCGEHAHCHEIAICIEJAJCJE...

#1: Protein ...
Tubulin alpha chain / Alpha-tubulin


Mass: 49639.035 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote)
References: UniProt: P41351, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein ...
Tubulin beta chain / Beta-tubulin


Mass: 49617.676 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: P41352
#3: Protein Sperm flagellar protein


Mass: 24702.463 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: Q22DM0
#4: Protein TLP1


Mass: 88103.156 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: I7M0H4
#5: Protein C2 domain protein


Mass: 57465.531 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: Q246A0
#6: Protein
CFAP213


Mass: 37998.410 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: I7M5Z8
#7: Protein TLP2


Mass: 205367.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: I7MHP2
#8: Protein Cation channel family protein


Mass: 39902.203 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: W7X235
#9: Protein
Dpy-30 motif protein


Mass: 11293.362 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote) / References: UniProt: Q22W95

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Protein/peptide , 1 types, 27 molecules 8A8B8C8D8E8F8G8H8I8J8K8L8M8N8O8P8Q8R8S8T8U8V8W8X8Y8Z9A

#10: Protein/peptide ...
Unknown


Mass: 3252.000 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila CU428 (eukaryote)

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Non-polymers , 3 types, 117 molecules

#11: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#12: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Mg
#13: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ciliary tip central pair / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#10 / Source: NATURAL
Source (natural)Organism: Tetrahymena thermophila CU428 (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66174 / Symmetry type: POINT

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