9I8M | pdb_00009i8m

NEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis, focused reconstruction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural mechanisms for centrosomal recruitment and organization of the microtubule nucleator gamma-TuRC.

Gao, Q.Hofer, F.W.Filbeck, S.Vermeulen, B.J.A.Wurtz, M.Neuner, A.Kaplan, C.Zezlina, M.Sala, C.Shin, H.Gruss, O.J.Schiebel, E.Pfeffer, S.

(2025) Nat Commun 16: 2453-2453

  • DOI: https://doi.org/10.1038/s41467-025-57729-2
  • Primary Citation of Related Structures:  
    9I8G, 9I8H, 9I8M, 9I8N

  • PubMed Abstract: 

    The γ-tubulin ring complex (γ-TuRC) acts as a structural template for microtubule formation at centrosomes, associating with two main compartments: the pericentriolar material and the centriole lumen. In the pericentriolar material, the γ-TuRC is involved in microtubule organization, while the function of the centriole lumenal pool remains unclear. The conformational landscape of the γ-TuRC, which is crucial for its activity, and its centrosomal anchoring mechanisms, which determine γ-TuRC activity and turnover, are not understood. Using cryo-electron tomography, we analyze γ-TuRCs in human cells and purified centrosomes. Pericentriolar γ-TuRCs simultaneously associate with the essential adapter NEDD1 and the microcephaly protein CDK5RAP2. NEDD1 forms a tetrameric structure at the γ-TuRC base through interactions with four GCP3/MZT1 modules and GCP5/6-specific extensions, while multiple copies of CDK5RAP2 engage the γ-TuRC in two distinct binding patterns to promote γ-TuRC closure and activation. In the centriole lumen, the microtubule branching factor Augmin tethers a condensed cluster of γ-TuRCs to the centriole wall with defined directional orientation. Centriole-lumenal γ-TuRC-Augmin is protected from degradation during interphase and released in mitosis to aid chromosome alignment. This study provides a unique view on γ-TuRC structure and molecular organization at centrosomes and identifies an important cellular function of centriole-lumenal γ-TuRCs.


  • Organizational Affiliation
    • Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component
A, C, E, G
896Xenopus laevisMutation(s): 0 
UniProt
Find proteins for A0A8J0T6B8 (Xenopus laevis)
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J0T6B8
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 3 homolog906Xenopus laevisMutation(s): 0 
UniProt
Find proteins for O73787 (Xenopus laevis)
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UniProt GroupO73787
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component
I, K
666Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q642S3 (Xenopus laevis)
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UniProt GroupQ642S3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component1,019Xenopus laevisMutation(s): 0 
UniProt
Find proteins for A0A1L8HGZ5 (Xenopus laevis)
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UniProt GroupA0A1L8HGZ5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 61,698Xenopus laevisMutation(s): 0 
UniProt
Find proteins for A0A8J0UR45 (Xenopus laevis)
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UniProt GroupA0A8J0UR45
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NEDD1 gamma-tubulin ring complex targeting factor L homeologR [auth U],
S [auth V],
T [auth W],
U [auth X]
671Xenopus laevisMutation(s): 0 
UniProt
Find proteins for A0A8J0Q0Y8 (Xenopus laevis)
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UniProt GroupA0A8J0Q0Y8
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitotic-spindle organizing protein 172Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q5U4M5 (Xenopus laevis)
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UniProt GroupQ5U4M5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyDFG Schi 295/4-4
German Research Foundation (DFG)GermanyDFG Schi 295/11-1
German Research Foundation (DFG)GermanyDFG PF 963/1-4
German Research Foundation (DFG)GermanyDFG PF 963/4-1
German Research Foundation (DFG)GermanyINST 35/1314-1 FUGG
German Research Foundation (DFG)GermanyINST 35/1503-1 FUGG
German Research Foundation (DFG)GermanyINST 35/1134-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-09
    Changes: Data collection