9QZF | pdb_00009qzf

Proximal A-C linker of Tetrahymena centriole, six repeating units

PDB DOI: https://doi.org/10.2210/pdb9QZF/pdb
EM Map EMD-53471: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Tetrahymena thermophila
Mutation(s): No

Deposited: 2025-04-22 Released: 2025-09-17
Deposition Author(s): Cai, B., Xu, J.W., Luo, L., Aarts, E., Leitner, A., Ishikawa, T., Beltro, P., Pilhofer, M., Wieczorek, M.
Funding Organization(s): ETH Zurich, Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure and assembly of the A-C linker connecting microtubule triplets in centrioles.

Cai, B., Xu, J., Collet, E.H., Aarts, E., Luo, L., Leitner, A., Ishikawa, T., Beltrao, P., Pearson, C.G., Pilhofer, M., Wieczorek, M.

(2025) Sci Adv 11: eady3689-eady3689

PubMed: 41061066 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.ady3689
Primary Citation Related Structures:
9QZC, 9QZF

PubMed 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-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.

Organizational Affiliation

Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 4,562.34 kDa
Atom Count: 130,144
Modeled Residue Count: 26,153
Deposited Residue Count: 41,052
Unique protein chains: 16

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat WRAP73-like protein, putative	A B [auth C] BD [auth CP] CA [auth i] FD [auth Ca] A, B [auth C], BD [auth CP], CA [auth i], FD [auth Ca], VB [auth BD]	452	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for I7MIG5 (Tetrahymena thermophila (strain SB210)) Explore I7MIG5 Go to UniProtKB: I7MIG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I7MIG5
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Centrosomal protein, putative	BA [auth f] C [auth D] DA [auth k] ED [auth CW] HA [auth q] BA [auth f], C [auth D], DA [auth k], ED [auth CW], HA [auth q], HD [auth Cd], IA [auth s], ID [auth Ch], JD [auth z], MA [auth y], WB [auth BK], YB [auth BR]	380	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for Q24GZ2 (Tetrahymena thermophila (strain SB210)) Explore Q24GZ2 Go to UniProtKB: Q24GZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q24GZ2
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab-GAP TBC domain-containing protein	AC [auth BY] D [auth E] FA [auth n] H [auth I] NA [auth 1] AC [auth BY], D [auth E], FA [auth n], H [auth I], NA [auth 1], RA [auth 7]	937	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for Q23K58 (Tetrahymena thermophila (strain SB210)) Explore Q23K58 Go to UniProtKB: Q23K58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q23K58
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	AA [auth d] BC [auth BZ] E [auth F] GA [auth o] LC [auth Bw] AA [auth d], BC [auth BZ], E [auth F], GA [auth o], LC [auth Bw], XB [auth BO]	151	Tetrahymena thermophila	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
TBC1 domain family member 31	CB [auth AO] DC [auth Bf] F [auth G] GB [auth AU] JC [auth Bt] CB [auth AO], DC [auth Bf], F [auth G], GB [auth AU], JC [auth Bt], K [auth L], KA [auth v], L [auth M], Q [auth R], SA [auth 9], UA [auth AB], WA [auth AE]	1,202	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for Q23AD1 (Tetrahymena thermophila (strain SB210)) Explore Q23AD1 Go to UniProtKB: Q23AD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q23AD1
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	EA [auth l] EC [auth Bg] G [auth H] LA [auth w] PC [auth B4] EA [auth l], EC [auth Bg], G [auth H], LA [auth w], PC [auth B4], ZB [auth BV]	164	Tetrahymena thermophila	Mutation(s): 0
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
POC1 centriolar protein homolog	BB [auth AM] GC [auth Bm] I [auth J] N [auth O] PA [auth 4] BB [auth AM], GC [auth Bm], I [auth J], N [auth O], PA [auth 4], XA [auth AG]	634	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for Q229Z6 (Tetrahymena thermophila (strain SB210)) Explore Q229Z6 Go to UniProtKB: Q229Z6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q229Z6
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	CC [auth Bc] HC [auth Bn] J [auth K] JA [auth t] QA [auth 5] CC [auth Bc], HC [auth Bn], J [auth K], JA [auth t], QA [auth 5], TC [auth CA]	167	Tetrahymena thermophila	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	FC [auth Bj] KC [auth Bu] M [auth N] OA [auth 2] VA [auth AC] FC [auth Bj], KC [auth Bu], M [auth N], OA [auth 2], VA [auth AC], XC [auth CH]	161	Tetrahymena thermophila	Mutation(s): 0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	HB [auth AW] KB [auth Ac] NC [auth B1] O [auth P] T [auth U] HB [auth AW], KB [auth Ac], NC [auth B1], O [auth P], T [auth U], ZA [auth AJ]	32	Tetrahymena thermophila	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	AB [auth AK] AD [auth CO] IC [auth Bq] OC [auth B2] P [auth Q] AB [auth AK], AD [auth CO], IC [auth Bq], OC [auth B2], P [auth Q], TA [auth 0]	105	Tetrahymena thermophila	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	EB [auth AR] LB [auth Ae] NB [auth Ak] R [auth S] RC [auth B8] EB [auth AR], LB [auth Ae], NB [auth Ak], R [auth S], RC [auth B8], W [auth X]	33	Tetrahymena thermophila	Mutation(s): 0
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	DD [auth CV] FB [auth AS] MC [auth Bx] S [auth T] SC [auth B9] DD [auth CV], FB [auth AS], MC [auth Bx], S [auth T], SC [auth B9], YA [auth AH]	127	Tetrahymena thermophila	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	IB [auth AZ] OB [auth Am] RB [auth As] U [auth V] VC [auth CE] IB [auth AZ], OB [auth Am], RB [auth As], U [auth V], VC [auth CE], Y [auth a]	153	Tetrahymena thermophila	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Protein Chain	DB [auth AP] GD [auth Cc] JB [auth Aa] QC [auth B5] V [auth W] DB [auth AP], GD [auth Cc], JB [auth Aa], QC [auth B5], V [auth W], WC [auth CF]	102	Tetrahymena thermophila	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
SWIM-type domain-containing protein	CD [auth CT] MB [auth Ai] PB [auth An] QB [auth Aq] SB [auth Av] CD [auth CT], MB [auth Ai], PB [auth An], QB [auth Aq], SB [auth Av], TB [auth Az], UB [auth A7], UC [auth CB], X [auth Z], YC [auth CI], Z [auth c], ZC [auth CM]	230	Tetrahymena thermophila	Mutation(s): 0
UniProt
Find proteins for I7LY02 (Tetrahymena thermophila (strain SB210)) Explore I7LY02 Go to UniProtKB: I7LY02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I7LY02
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Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK Query on UNK	AA [auth d] BC [auth BZ] E [auth F] GA [auth o] LC [auth Bw] AA [auth d], BC [auth BZ], E [auth F], GA [auth o], LC [auth Bw], XB [auth BO]	L-PEPTIDE LINKING	C₄ H₉ N O₂		--