5JW7

Crystal structure of SopA-Trim56 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

Starting Models: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural basis for the recognition and degradation of host TRIM proteins by Salmonella effector SopA.

Fiskin, E.Bhogaraju, S.Herhaus, L.Kalayil, S.Hahn, M.Dikic, I.

(2017) Nat Commun 8: 14004-14004

  • DOI: https://doi.org/10.1038/ncomms14004
  • Primary Citation of Related Structures:  
    5JW7

  • PubMed Abstract: 

    The hallmark of Salmonella Typhimurium infection is an acute intestinal inflammatory response, which is mediated through the action of secreted bacterial effector proteins. The pro-inflammatory Salmonella effector SopA is a HECT-like E3 ligase, which was previously proposed to activate host RING ligases TRIM56 and TRIM65. Here we elucidate an inhibitory mechanism of TRIM56 and TRIM65 targeting by SopA. We present the crystal structure of SopA in complex with the RING domain of human TRIM56, revealing the atomic details of their interaction and the basis for SopA selectivity towards TRIM56 and TRIM65. Structure-guided biochemical analysis shows that SopA inhibits TRIM56 E3 ligase activity by occluding the E2-interacting surface of TRIM56. We further demonstrate that SopA ubiquitinates TRIM56 and TRIM65, resulting in their proteasomal degradation during infection. Our results provide the basis for how a bacterial HECT ligase blocks host RING ligases and exemplifies the multivalent power of bacterial effectors during infection.


  • Organizational Affiliation

    Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase SopA282Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: sopASTM2066
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt
Find proteins for Q8ZNR3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZNR3 
Go to UniProtKB:  Q8ZNR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZNR3
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 TRIM5693Homo sapiensMutation(s): 0 
Gene Names: TRIM56RNF109
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRZ2 (Homo sapiens)
Explore Q9BRZ2 
Go to UniProtKB:  Q9BRZ2
PHAROS:  Q9BRZ2
GTEx:  ENSG00000169871 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRZ2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.015α = 90
b = 71.015β = 90
c = 122.944γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description