7Y3B

Crystal structure of TRIM7 bound to GN1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

C-terminal glutamine acts as a C-degron targeted by E3 ubiquitin ligase TRIM7.

Ru, Y.Yan, X.Zhang, B.Song, L.Feng, Q.Ye, C.Zhou, Z.Yang, Z.Li, Y.Zhang, Z.Li, Q.Mi, W.Dong, C.

(2022) Proc Natl Acad Sci U S A 119: e2203218119-e2203218119

  • DOI: https://doi.org/10.1073/pnas.2203218119
  • Primary Citation of Related Structures:  
    7Y3A, 7Y3B, 7Y3C

  • PubMed Abstract: 

    The exposed N-terminal or C-terminal residues of proteins can act, in cognate sequence contexts, as degradation signals (degrons) that are targeted by specific E3 ubiquitin ligases for proteasome-dependent degradation by N -degron or C-degron pathways. Here, we discovered a distinct C-degron pathway, termed the Gln/C-degron pathway, in which the B30.2 domain of E3 ubiquitin ligase TRIM7 (TRIM7 B30.2 ) mediates the recognition of proteins bearing a C-terminal glutamine. By determining crystal structures of TRIM7 B30.2 in complexes with various peptides, we show that TRIM7 B30.2 forms a positively charged binding pocket to engage the "U"-shaped Gln/C-degron. The four C-terminal residues of a substrate play an important role in C-degron recognition, with C-terminal glutamine as the principal determinant. In vitro biochemical and cellular experiments were used to further analyze the substrate specificity and selective degradation of the Gln/C-degron by TRIM7.


  • Organizational Affiliation

    Haihe Laboratory of Cell Ecosystem, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300070, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM7,TRIM7-GN1191Homo sapiensMutation(s): 0 
Gene Names: TRIM7GNIPRNF90
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C029 (Homo sapiens)
Explore Q9C029 
Go to UniProtKB:  Q9C029
PHAROS:  Q9C029
GTEx:  ENSG00000146054 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C029
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.768α = 90
b = 79.768β = 90
c = 52.229γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31900865
National Natural Science Foundation of China (NSFC)China32071193
National Natural Science Foundation of China (NSFC)China81874039

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description