9H6W | pdb_00009h6w

Crystal structure of the Salmonella effector SspH1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.316 (Depositor), 0.316 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

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


Literature

Conformational dynamics of the bacterial E3 ligase SspH1.

Kennedy, C.R.Esposito, D.Huber, J.House, D.Rittinger, K.

(2025) J Biological Chem 301: 110671-110671

  • DOI: https://doi.org/10.1016/j.jbc.2025.110671
  • Primary Citation of Related Structures:  
    9H6W

  • PubMed Abstract: 

    The SspH/IpaH family of novel E3 ligases are found in a number of Gram-negative bacteria and are used to target host enzymes for degradation to support pathogenesis. These E3 enzymes are autoinhibited in the absence of substrate, and different models for release of autoinhibition have been suggested. However, many of the molecular details of individual steps during the ubiquitin (Ub) transfer reaction remain unknown. Here, we present the crystal structure of Salmonella SspH1 and an analysis of the solution properties of SspH1 on its own and in complex with substrate and Ub. Our data show that SspH1 exists in a conformational equilibrium between open and closed states and that substrate binding only modulates the distribution of these states but does not induce major conformational changes. This suggests that additional mechanisms must exist to bring the substrates close to the active site to mediate transfer of Ub from the E3-Ub conjugate.


  • Organizational Affiliation
    • Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase SspH1540Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: sspH1STM14_1483
EC: 2.3.2.27
UniProt
Find proteins for D0ZVG2 (Salmonella typhimurium (strain 14028s / SGSC 2262))
Explore D0ZVG2 
Go to UniProtKB:  D0ZVG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0ZVG2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TLA (Subject of Investigation/LOI)
Query on TLA

Download Ideal Coordinates CCD File 
B [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.316 (Depositor), 0.316 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.772α = 90
b = 170.772β = 90
c = 94.8γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomCC2075
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T014547/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references