8A58

X-ray structure of TRIM21 RING E3 ligase in complex with E2 enzyme Ube2W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Trim-Away ubiquitinates and degrades lysine-less and N-terminally acetylated substrates.

Kiss, L.Rhinesmith, T.Luptak, J.Dickson, C.F.Weidenhausen, J.Smyly, S.Yang, J.C.Maslen, S.L.Sinning, I.Neuhaus, D.Clift, D.James, L.C.

(2023) Nat Commun 14: 2160-2160

  • DOI: https://doi.org/10.1038/s41467-023-37504-x
  • Primary Citation of Related Structures:  
    8A58

  • PubMed Abstract: 

    TRIM proteins are the largest family of E3 ligases in mammals. They include the intracellular antibody receptor TRIM21, which is responsible for mediating targeted protein degradation during Trim-Away. Despite their importance, the ubiquitination mechanism of TRIM ligases has remained elusive. Here we show that while Trim-Away activation results in ubiquitination of both ligase and substrate, ligase ubiquitination is not required for substrate degradation. N-terminal TRIM21 RING ubiquitination by the E2 Ube2W can be inhibited by N-terminal acetylation, but this doesn't prevent substrate ubiquitination nor degradation. Instead, uncoupling ligase and substrate degradation prevents ligase recycling and extends functional persistence in cells. Further, Trim-Away degrades substrates irrespective of whether they contain lysines or are N-terminally acetylated, which may explain the ability of TRIM21 to counteract fast-evolving pathogens and degrade diverse substrates.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. lkiss@biochem.mpg.de.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 WA,
D [auth B]
153Homo sapiensMutation(s): 0 
Gene Names: UBE2WUBC16
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.25 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96B02 (Homo sapiens)
Explore Q96B02 
Go to UniProtKB:  Q96B02
PHAROS:  Q96B02
GTEx:  ENSG00000104343 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96B02
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM21B [auth C],
C [auth D]
85Homo sapiensMutation(s): 0 
Gene Names: TRIM21RNF81RO52SSA1
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P19474 (Homo sapiens)
Explore P19474 
Go to UniProtKB:  P19474
PHAROS:  P19474
GTEx:  ENSG00000132109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19474
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.82α = 90
b = 75.482β = 119.31
c = 63.835γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description