8IMS

Crystal structure of TRAF7 coiled-coil domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 

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

The structure of TRAF7 coiled-coil trimer provides insight into its function in zebrafish embryonic development.

Song, X.Hu, R.Chen, Y.Xiao, M.Zhang, H.Wu, S.Lu, Q.

(2024) J Mol Cell Biol 16

  • DOI: https://doi.org/10.1093/jmcb/mjad083
  • Primary Citation of Related Structures:  
    8IMS

  • PubMed Abstract: 

    TRAF7 serves as a crucial intracellular adaptor and E3 ubiquitin ligase involved in signal transduction pathways, contributing to immune responses, tumor progression, and embryonic development. Somatic mutations within the coiled-coil (CC) domain and WD40 repeat domain of TRAF7 could cause brain tumors, while germline pathogenic mutations contribute to severe developmental abnormalities. However, the precise molecular mechanism underlying TRAF7 involvement in embryonic development remains unclear. In this study, we employed zebrafish as an in-vivo model system. TRAF7 knockdown caused defects in zebrafish embryonic development. We determined the crystal structure of TRAF7 CC domain at 3.3 Å resolution and found that the CC region trimerization was essential for TRAF7 functionality during zebrafish embryonic development. Additionally, disease-causing mutations in TRAF7 CC region could impair the trimer formation, consequently impacting early embryonic development of zebrafish. Therefore, our study sheds light on the molecular mechanism of TRAF7 CC trimer formation and its pivotal role in embryonic development.


  • Organizational Affiliation

    Molecular Diagnostic Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200040, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRAF7A [auth B],
B [auth A],
C
121Homo sapiensMutation(s): 0 
Gene Names: TRAF7RFWD1RNF119
EC: 2.3.2.27 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6Q0C0 (Homo sapiens)
Explore Q6Q0C0 
Go to UniProtKB:  Q6Q0C0
PHAROS:  Q6Q0C0
GTEx:  ENSG00000131653 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6Q0C0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.923α = 90
b = 169.923β = 90
c = 57.055γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaYG2019QNB01

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Database references