9G09 | pdb_00009g09

Structure of human RNF213 bound to the secreted effector IpaH2.5 from Shigella flexneri


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9G09

This is version 1.3 of the entry. See complete history

Literature

Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213.

Naydenova, K.Boyle, K.B.Pathe, C.Pothukuchi, P.Crespillo-Casado, A.Scharte, F.Hammoudi, P.M.Otten, E.G.Alto, N.M.Randow, F.

(2025) Nat Struct Mol Biol 32: 1741-1751

  • DOI: https://doi.org/10.1038/s41594-025-01530-8
  • Primary Citation Related Structures: 
    9G08, 9G09

  • PubMed Abstract: 

    Pathogens have evolved diverse strategies to counteract host immunity. Ubiquitylation of lipopolysaccharide (LPS) on cytosol-invading bacteria by the E3 ligase RNF213 creates 'eat me' signals for antibacterial autophagy, but whether and how cytosol-adapted bacteria avoid LPS ubiquitylation remains poorly understood. Here, we show that the enterobacterium Shigella flexneri actively antagonizes LPS ubiquitylation through IpaH1.4, a secreted effector protein with ubiquitin E3 ligase activity. IpaH1.4 binds to RNF213, ubiquitylates it and targets it for proteasomal degradation, thus counteracting host-protective LPS ubiquitylation. To understand how IpaH1.4 recognizes RNF213, we determined the cryogenic electron microscopy structure of the IpaH1.4-RNF213 complex. The specificity of the interaction is achieved through the leucine-rich repeat of IpaH1.4, which binds the RING domain of RNF213 by hijacking the conserved RING interface required for binding to ubiquitin-charged E2 enzymes. IpaH1.4 also targets other E3 ligases involved in inflammation and immunity through binding to the E2-interacting face of their RING domains, including the E3 ligase LUBAC that is required for the synthesis of M1-linked ubiquitin chains on cytosol-invading bacteria downstream of RNF213. We conclude that IpaH1.4 has evolved to antagonize multiple antibacterial and proinflammatory host E3 ligases.


  • Organizational Affiliation
    • Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 660.83 kDa 
  • Atom Count: 38,435 
  • Modeled Residue Count: 4,766 
  • Deposited Residue Count: 5,810 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase IpaH2.5A [auth B]563Shigella flexneri 5a str. M90TMutation(s): 0 
Gene Names: ipaH2.5SF_p0054
EC: 2.3.2.27
UniProt
Find proteins for A0A0H2USC0 (Shigella flexneri)
Explore A0A0H2USC0 
Go to UniProtKB:  A0A0H2USC0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2USC0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF213B [auth A]5,247Homo sapiensMutation(s): 0 
Gene Names: RNF213ALO17C17orf27KIAA1554KIAA1618MYSTR
EC: 2.3.2.27 (PDB Primary Data), 3.6.4 (PDB Primary Data), 2.3.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q63HN8 (Homo sapiens)
Explore Q63HN8 
Go to UniProtKB:  Q63HN8
PHAROS:  Q63HN8
GTEx:  ENSG00000173821 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63HN8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomU105170648
Wellcome TrustUnited Kingdom222503/Z/21/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-09
    Changes: Data collection
  • Version 1.3: 2025-10-01
    Changes: Data collection, Database references