9JWG | pdb_00009jwg

Cryo-EM Focused Refined Map of Human RNF213 E3 module and IpaH1.4 LRR domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Shigella effector IpaH1.4 subverts host E3 ligase RNF213 to evade antibacterial immunity.

Zhou, X.Zhang, H.Wang, Y.Wang, D.Lin, Z.Zhang, Y.Tang, Y.Liu, J.Yao, Y.F.Zhang, Y.Pan, L.

(2025) Nat Commun 16: 3099-3099

  • DOI: https://doi.org/10.1038/s41467-025-58432-y
  • Primary Citation of Related Structures:  
    9JTA, 9JW1, 9JWG

  • PubMed Abstract: 

    Ubiquitination plays vital roles in modulating pathogen-host cell interactions. RNF213, a E3 ligase, can catalyze the ubiquitination of lipopolysaccharide (LPS) and is crucial for antibacterial immunity in mammals. Shigella flexneri, an LPS-containing pathogenic bacterium, has developed mechanisms to evade host antibacterial defenses during infection. However, the precise strategies by which S. flexneri circumvents RNF213-mediated antibacterial immunity remain poorly understood. Here, through comprehensive biochemical, structural and cellular analyses, we reveal that the E3 effector IpaH1.4 of S. flexneri can directly target human RNF213 via a specific interaction between the IpaH1.4 LRR domain and the RING domain of RNF213, and mediate the ubiquitination and proteasomal degradation of RNF213 in cells. Furthermore, we determine the cryo-EM structure of human RNF213 and the crystal structure of the IpaH1.4 LRR/RNF213 RING complex, elucidating the molecular mechanism underlying the specific recognition of RNF213 by IpaH1.4. Finally, our cell based functional assays demonstrate that the targeting of host RNF213 by IpaH1.4 promotes S. flexneri proliferation within infected cells. In summary, our work uncovers an unprecedented strategy employed by S. flexneri to subvert the key host immune factor RNF213, thereby facilitating bacterial proliferation during invasion.


  • Organizational Affiliation
    • State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase IpaH1.4A [auth B]579Shigella flexneriMutation(s): 0 
Gene Names: ipaH1.4SF_p0265
EC: 2.3.2.27
UniProt
Find proteins for A0A0H2USG1 (Shigella flexneri)
Explore A0A0H2USG1 
Go to UniProtKB:  A0A0H2USG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2USG1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ring finger protein 213B [auth A]4,841Homo sapiensMutation(s): 0 
Gene Names: RNF213
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0A0MTR7 (Homo sapiens)
Explore A0A0A0MTR7 
Go to UniProtKB:  A0A0A0MTR7
GTEx:  ENSG00000173821 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A0MTR7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-05-07 
  • Deposition Author(s): Zhang, H.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071219

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release