[English] 日本語
Yorodumi
- PDB-9qzc: Proximal A-C linker of Tetrahymena centriole, one repeating unit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qzc
TitleProximal A-C linker of Tetrahymena centriole, one repeating unit
Components
  • (Unknown Protein ...) x 9
  • Centrosomal protein, putative
  • POC1 centriolar protein homolog
  • Rab-GAP TBC domain-containing protein
  • SWIM-type domain-containing protein
  • TBC1 domain family member 31
  • WD repeat WRAP73-like protein, putative
KeywordsSTRUCTURAL PROTEIN / centriole / basal body / centrosome
Function / homology
Function and homology information


MWP complex / cell projection organization / centrosome cycle / microtubule organizing center / cilium assembly / centriole / centriolar satellite / ciliary basal body / centrosome / cytoplasm
Similarity search - Function
: / : / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / : / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...: / : / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / : / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
SWIM-type domain-containing protein / WD repeat WRAP73-like protein, putative / POC1 centriolar protein homolog / TBC1 domain family member 31 / Rab-GAP TBC domain-containing protein / Centrosomal protein, putative
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsCai, B. / Xu, J.W. / Luo, L. / Aarts, E. / Leitner, A. / Ishikawa, T. / Beltro, P. / Pilhofer, M. / Wieczorek, M.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
ETH ZurichETH-22 22-1 Switzerland
Swiss National Science Foundation320030-231677 Switzerland
Swiss National Science FoundationIZLIZ3 200294 Switzerland
CitationJournal: Sci Adv / Year: 2025
Title: Structure and assembly of the A-C linker connecting microtubule triplets in centrioles.
Authors: Bin Cai / Jingwei Xu / Erik H Collet / Ellen Aarts / Leo Luo / Alexander Leitner / Takashi Ishikawa / Pedro Beltrao / Chad G Pearson / Martin Pilhofer / Michal Wieczorek /
Abstract: Centriole assembly involves the coordination of centriolar modules. One module is the A-C linker, an enigmatic protein assembly connecting the A-microtubule of one microtubule triplet to the C- ...Centriole assembly involves the coordination of centriolar modules. One module is the A-C linker, an enigmatic protein assembly connecting the A-microtubule of one microtubule triplet to the C-microtubule of the neighboring triplet. Here, we integrated biochemistry, multiscale cryo-electron microscopy, and AlphaFold modeling to investigate the architecture of the centriole. Using an improved centriole isolation method, we determined the structure of the A-C linker bound to microtubule triplets, which revealed how the A-C linker cross-links microtubules and integrates with the B-C junction. We found marked changes in the structure and composition of the A-C linker that correlate with the presence of other centriolar modules, including the pinhead, cartwheel, and inner scaffold. Our findings show that the A-C linker is a highly integrated component of the centriole whose polymorphism may orchestrate the assembly of spatially distinct centriolar modules, and provide a framework for dissecting the biology of centrioles.
History
DepositionApr 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
i: WD repeat WRAP73-like protein, putative
q: Centrosomal protein, putative
y: Centrosomal protein, putative
7: Rab-GAP TBC domain-containing protein
AE: TBC1 domain family member 31
AM: POC1 centriolar protein homolog
AU: TBC1 domain family member 31
Ac: Unknown Protein Chain
As: Unknown Protein Chain
Az: SWIM-type domain-containing protein
A7: SWIM-type domain-containing protein
Bw: Unknown Protein Chain
B4: Unknown Protein Chain
CA: Unknown Protein Chain
CH: Unknown Protein Chain
CO: Unknown Protein Chain
CV: Unknown Protein Chain
Cc: Unknown Protein Chain


Theoretical massNumber of molelcules
Total (without water)757,56318
Polymers757,56318
Non-polymers00
Water00
1


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

-
Components

-
Protein , 6 types, 9 molecules iqy7AEAUAMAzA7

#1: Protein WD repeat WRAP73-like protein, putative


Mass: 51977.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MIG5
#2: Protein Centrosomal protein, putative


Mass: 44594.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24GZ2
#3: Protein Rab-GAP TBC domain-containing protein


Mass: 110098.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23K58
#4: Protein TBC1 domain family member 31


Mass: 141643.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23AD1
#5: Protein POC1 centriolar protein homolog


Mass: 71408.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q229Z6
#8: Protein SWIM-type domain-containing protein


Mass: 26274.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LY02

-
Unknown Protein ... , 9 types, 9 molecules AcAsBwB4CACHCOCVCc

#6: Protein/peptide Unknown Protein Chain


Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#7: Protein Unknown Protein Chain


Mass: 13039.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#9: Protein Unknown Protein Chain


Mass: 12868.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#10: Protein Unknown Protein Chain


Mass: 13975.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#11: Protein Unknown Protein Chain


Mass: 14230.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#12: Protein Unknown Protein Chain


Mass: 13719.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#13: Protein Unknown Protein Chain


Mass: 8954.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#14: Protein Unknown Protein Chain


Mass: 10826.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#15: Protein Unknown Protein Chain


Mass: 8698.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: proximal A-C linker of Tetrahymena thermophila basal body centriole
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
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: 800 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155485 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more