9I8H | pdb_00009i8h

Outwards conformation' of the human gamma-TuRC from purified centrosomes obtained by rigid body docking

  • Classification: CELL CYCLE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-02-04 Released: 2025-03-19 
  • Deposition Author(s): Hofer, F.W., Pfeffer, S.
  • Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 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 2
A, C, E, G, M
902Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSJ2 (Homo sapiens)
Explore Q9BSJ2 
Go to UniProtKB:  Q9BSJ2
PHAROS:  Q9BSJ2
GTEx:  ENSG00000130640 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BSJ2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 3907Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CW5 (Homo sapiens)
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PHAROS:  Q96CW5
GTEx:  ENSG00000126216 
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UniProt GroupQ96CW5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 4
I, K
667Homo sapiensMutation(s): 0 
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Find proteins for Q9UGJ1 (Homo sapiens)
Explore Q9UGJ1 
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PHAROS:  Q9UGJ1
GTEx:  ENSG00000137822 
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UniProt GroupQ9UGJ1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 51,024Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RT8 (Homo sapiens)
Explore Q96RT8 
Go to UniProtKB:  Q96RT8
PHAROS:  Q96RT8
GTEx:  ENSG00000275835 
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UniProt GroupQ96RT8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 6
L, P
1,819Homo sapiensMutation(s): 0 
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PHAROS:  Q96RT7
GTEx:  ENSG00000128159 
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UniProt GroupQ96RT7
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1O [auth U]376Homo sapiensMutation(s): 0 
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens)
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PHAROS:  P60709
GTEx:  ENSG00000075624 
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UniProt GroupP60709
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitotic-spindle organizing protein 1
Q, S
82Homo sapiensMutation(s): 0 
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Find proteins for Q08AG7 (Homo sapiens)
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PHAROS:  Q08AG7
GTEx:  ENSG00000204899 
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UniProt GroupQ08AG7
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin gamma-1 chain451Homo sapiensMutation(s): 0 
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Find proteins for P23258 (Homo sapiens)
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PHAROS:  P23258
GTEx:  ENSG00000131462 
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UniProt GroupP23258
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
IA [auth a]
JA [auth b]
KA [auth c]
LA [auth d]
MA [auth e]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
HA [auth U]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

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

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