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- PDB-9qzc: Proximal A-C linker of Tetrahymena centriole, one repeating unit -

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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: To Be Published
Title: Structure and assembly of the A-C linker connecting microtubule triplets in centrioles
Authors: Cai, B. / Xu, J. / Aarts, E. / Luo, L. / Leitner, A. / Ishikawa, T. / Beltro, P. / Pilhofer, M. / Wieczorek, M.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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)

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Details

Has protein modificationN

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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: 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

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

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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

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