9I8G | pdb_00009i8g

Inwards 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: 22.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: experimental
View more details

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


  • Organizational Affiliation

    Zentrum f¨¹r Molekulare Biologie der Universit?t Heidelberg (ZMBH), Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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 3
B,
D,
F,
H,
N [auth T],
R
907Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CW5 (Homo sapiens)
Explore Q96CW5 
Go to UniProtKB:  Q96CW5
PHAROS:  Q96CW5
GTEx:  ENSG00000126216 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96CW5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 4
I, K
667Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGJ1 (Homo sapiens)
Explore Q9UGJ1 
Go to UniProtKB:  Q9UGJ1
PHAROS:  Q9UGJ1
GTEx:  ENSG00000137822 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGJ1
Sequence Annotations
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  • Reference Sequence
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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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RT8
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 6
L, P
1,819Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RT7 (Homo sapiens)
Explore Q96RT7 
Go to UniProtKB:  Q96RT7
PHAROS:  Q96RT7
GTEx:  ENSG00000128159 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RT7
Sequence Annotations
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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)
Explore P60709 
Go to UniProtKB:  P60709
PHAROS:  P60709
GTEx:  ENSG00000075624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60709
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitotic-spindle organizing protein 1
Q, S
82Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q08AG7 (Homo sapiens)
Explore Q08AG7 
Go to UniProtKB:  Q08AG7
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 
UniProt & NIH Common Fund Data Resources
Find proteins for P23258 (Homo sapiens)
Explore P23258 
Go to UniProtKB:  P23258
PHAROS:  P23258
GTEx:  ENSG00000131462 
Entity Groups  
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UniProt GroupP23258
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  • Reference Sequence
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]
IA [auth a],
JA [auth b],
KA [auth c],
LA [auth d],
MA [auth e],
NA [auth f],
OA [auth g],
PA [auth h],
QA [auth i],
RA [auth j],
SA [auth k],
TA [auth l],
UA [auth m],
VA [auth t]
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: 22.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



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
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