9QVM | pdb_00009qvm

Cryo-EM reconstruction of the NEDD1 anchor protein and CDK5RAP2 bound to the gamma-tubulin ring complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the microtubule-anchoring factor NEDD1 bound to the gamma-tubulin ring complex.

Munoz-Hernandez, H.Xu, Y.Pellicer Camardiel, A.Zhang, D.Xue, A.Aher, A.Walker, E.Marxer, F.Kapoor, T.M.Wieczorek, M.

(2025) J Cell Biol 224

  • DOI: https://doi.org/10.1083/jcb.202410206
  • Primary Citation of Related Structures:  
    9QVM, 9QVN

  • PubMed Abstract: 

    The γ-tubulin ring complex (γ-TuRC) is an essential multiprotein assembly that provides a template for microtubule nucleation. The γ-TuRC is recruited to microtubule-organizing centers (MTOCs) by the evolutionarily conserved attachment factor NEDD1. However, the structural basis of the NEDD1-γ-TuRC interaction is not known. Here, we report cryo-EM structures of NEDD1 bound to the human γ-TuRC in the absence or presence of the activating factor CDK5RAP2. We found that the C-terminus of NEDD1 forms a tetrameric α-helical assembly that contacts the lumen of the γ-TuRC cone and orients its microtubule-binding domain away from the complex. The structure of the γ-TuRC simultaneously bound to NEDD1 and CDK5RAP2 reveals that both factors can associate with the "open" conformation of the complex. Our results show that NEDD1 does not induce substantial conformational changes in the γ-TuRC but suggest that anchoring of γ-TuRC-capped microtubules by NEDD1 would be structurally compatible with the significant conformational changes experienced by the γ-TuRC during microtubule nucleation.


  • Organizational Affiliation
    • Institute of Molecular Biology and Biophysics, ETH Zürich , Zürich, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 3907Homo sapiensMutation(s): 0 
Gene Names: TUBGCP3GCP3
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitotic-spindle organizing protein 182Homo sapiensMutation(s): 0 
Gene Names: MZT1C13orf37MOZART1
UniProt & NIH Common Fund Data Resources
Find proteins for Q08AG7 (Homo sapiens)
Explore Q08AG7 
Go to UniProtKB:  Q08AG7
PHAROS:  Q08AG7
GTEx:  ENSG00000204899 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08AG7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NEDD1JA [auth V],
K [auth W],
KA [auth Y],
L [auth X]
660Homo sapiensMutation(s): 0 
Gene Names: NEDD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHV4 (Homo sapiens)
Explore Q8NHV4 
Go to UniProtKB:  Q8NHV4
PHAROS:  Q8NHV4
GTEx:  ENSG00000139350 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NHV4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1, N-terminally processedM [auth Z]375Homo sapiensMutation(s): 0 
Gene Names: ACTB
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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin gamma-1 chain457Homo sapiensMutation(s): 0 
Gene Names: TUBG1TUBG
UniProt & NIH Common Fund Data Resources
Find proteins for P23258 (Homo sapiens)
Explore P23258 
Go to UniProtKB:  P23258
PHAROS:  P23258
GTEx:  ENSG00000131462 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23258
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 4GA [auth K],
RA [auth I]
667Homo sapiensMutation(s): 0 
Gene Names: TUBGCP476PGCP4
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of Gamma-tubulin complex component 2LA [auth G],
NA [auth C],
PA [auth A],
QA [auth E],
SA [auth M]
930Homo sapiensMutation(s): 0 
Gene Names: TUBGCP2GCP2
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
TUBGCP6 proteinMA [auth L]1,811Homo sapiensMutation(s): 0 
Gene Names: TUBGCP6
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-tubulin complex component 5OA [auth J]1,024Homo sapiensMutation(s): 0 
Gene Names: TUBGCP5GCP5KIAA1899
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitotic-spindle organizing protein 2BTA [auth p]158Homo sapiensMutation(s): 0 
Gene Names: MZT2BFAM128BMOZART2B
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NZ67 (Homo sapiens)
Explore Q6NZ67 
Go to UniProtKB:  Q6NZ67
PHAROS:  Q6NZ67
GTEx:  ENSG00000152082 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NZ67
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
CDK5 regulatory subunit-associated protein 2UA [auth x],
VA [auth w]
1,663Homo sapiensMutation(s): 0 
Gene Names: CDK5RAP2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0A0MRG9 (Homo sapiens)
Explore A0A0A0MRG9 
Go to UniProtKB:  A0A0A0MRG9
GTEx:  ENSG00000136861 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A0MRG9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_208120
Swiss National Science FoundationSwitzerlandTMSGI3_211309

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection, Database references