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- PDB-9qzf: Proximal A-C linker of Tetrahymena centriole, six repeating units -

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Basic information

Entry
Database: PDB / ID: 9qzf
TitleProximal A-C linker of Tetrahymena centriole, six repeating units
Components
  • (Unknown Protein ...) x 10
  • 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.W. / Luo, L. / Aarts, E. / 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

Downloads & links

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Assembly

Deposited unit
A: WD repeat WRAP73-like protein, putative
C: WD repeat WRAP73-like protein, putative
D: Centrosomal protein, putative
E: Rab-GAP TBC domain-containing protein
F: Unknown Protein Chain
G: TBC1 domain family member 31
H: Unknown Protein Chain
I: Rab-GAP TBC domain-containing protein
J: POC1 centriolar protein homolog
K: Unknown Protein Chain
L: TBC1 domain family member 31
M: TBC1 domain family member 31
N: Unknown Protein Chain
O: POC1 centriolar protein homolog
P: Unknown Protein Chain
Q: Unknown Protein Chain
R: TBC1 domain family member 31
S: Unknown Protein Chain
T: Unknown Protein Chain
U: Unknown Protein Chain
V: Unknown Protein Chain
W: Unknown Protein Chain
X: Unknown Protein Chain
Z: SWIM-type domain-containing protein
a: Unknown Protein Chain
c: SWIM-type domain-containing protein
d: Unknown Protein Chain
f: Centrosomal protein, putative
i: WD repeat WRAP73-like protein, putative
k: Centrosomal protein, putative
l: Unknown Protein Chain
n: Rab-GAP TBC domain-containing protein
o: Unknown Protein Chain
q: Centrosomal protein, putative
s: Centrosomal protein, putative
t: Unknown Protein Chain
v: TBC1 domain family member 31
w: Unknown Protein Chain
y: Centrosomal protein, putative
1: Rab-GAP TBC domain-containing protein
2: Unknown Protein Chain
4: POC1 centriolar protein homolog
5: Unknown Protein Chain
7: Rab-GAP TBC domain-containing protein
9: TBC1 domain family member 31
0: Unknown Protein Chain
AB: TBC1 domain family member 31
AC: Unknown Protein Chain
AE: TBC1 domain family member 31
AG: POC1 centriolar protein homolog
AH: Unknown Protein Chain
AJ: Unknown Protein Chain
AK: Unknown Protein Chain
AM: POC1 centriolar protein homolog
AO: TBC1 domain family member 31
AP: Unknown Protein Chain
AR: Unknown Protein Chain
AS: Unknown Protein Chain
AU: TBC1 domain family member 31
AW: Unknown Protein Chain
AZ: Unknown Protein Chain
Aa: Unknown Protein Chain
Ac: Unknown Protein Chain
Ae: Unknown Protein Chain
Ai: SWIM-type domain-containing protein
Ak: Unknown Protein Chain
Am: Unknown Protein Chain
An: SWIM-type domain-containing protein
Aq: SWIM-type domain-containing protein
As: Unknown Protein Chain
Av: SWIM-type domain-containing protein
Az: SWIM-type domain-containing protein
A7: SWIM-type domain-containing protein
BD: WD repeat WRAP73-like protein, putative
BK: Centrosomal protein, putative
BO: Unknown Protein Chain
BR: Centrosomal protein, putative
BV: Unknown Protein Chain
BY: Rab-GAP TBC domain-containing protein
BZ: Unknown Protein Chain
Bc: Unknown Protein Chain
Bf: TBC1 domain family member 31
Bg: Unknown Protein Chain
Bj: Unknown Protein Chain
Bm: POC1 centriolar protein homolog
Bn: Unknown Protein Chain
Bq: Unknown Protein Chain
Bt: TBC1 domain family member 31
Bu: Unknown Protein Chain
Bw: Unknown Protein Chain
Bx: Unknown Protein Chain
B1: Unknown Protein Chain
B2: Unknown Protein Chain
B4: Unknown Protein Chain
B5: Unknown Protein Chain
B8: Unknown Protein Chain
B9: Unknown Protein Chain
CA: Unknown Protein Chain
CB: SWIM-type domain-containing protein
CE: Unknown Protein Chain
CF: Unknown Protein Chain
CH: Unknown Protein Chain
CI: SWIM-type domain-containing protein
CM: SWIM-type domain-containing protein
CO: Unknown Protein Chain
CP: WD repeat WRAP73-like protein, putative
CT: SWIM-type domain-containing protein
CV: Unknown Protein Chain
CW: Centrosomal protein, putative
Ca: WD repeat WRAP73-like protein, putative
Cc: Unknown Protein Chain
Cd: Centrosomal protein, putative
Ch: Centrosomal protein, putative
z: Centrosomal protein, putative


Theoretical massNumber of molelcules
Total (without water)4,562,338114
Polymers4,562,338114
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, 54 molecules ACiBDCPCaDfkqsyBKBRCWCdChzEIn17BYGLMRv9...

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


Mass: 51977.465 Da / Num. of mol.: 6 / 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.: 12 / 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.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23K58
#5: Protein
TBC1 domain family member 31


Mass: 141643.859 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23AD1
#7: Protein
POC1 centriolar protein homolog


Mass: 71408.133 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q229Z6
#16: Protein
SWIM-type domain-containing protein


Mass: 26274.373 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LY02

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Unknown Protein ... , 10 types, 60 molecules FdoBOBZBwHlwBVBgB4Kt5BcBnCAN2ACBjBuCHPUAJAWAcB1...

#4: Protein
Unknown Protein Chain


Mass: 12868.854 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#6: Protein
Unknown Protein Chain


Mass: 13975.214 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#8: Protein
Unknown Protein Chain


Mass: 14230.525 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#9: Protein
Unknown Protein Chain


Mass: 13719.902 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#10: Protein/peptide
Unknown Protein Chain


Mass: 2741.370 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#11: Protein
Unknown Protein Chain


Mass: 8954.028 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#12: Protein/peptide
Unknown Protein Chain


Mass: 2826.475 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#13: Protein
Unknown Protein Chain


Mass: 10826.337 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#14: Protein
Unknown Protein Chain


Mass: 13039.064 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#15: Protein
Unknown Protein Chain


Mass: 8698.714 Da / Num. of mol.: 6 / 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: #1-#2, #4, #6-#16, #3, #5 / 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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