9JTA | pdb_00009jta

Crystal structure of RNF213 RING domain bound to IpaH1.4 LRR domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.220 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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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
RING-type E3 ubiquitin transferaseA [auth B]235Shigella flexneri 5a str. M90TMutation(s): 0 
Gene Names: EKN05_024115
EC: 2.3.2.27
UniProt
Find proteins for A0A4P7TTK5 (Shigella flexneri serotype 5a (strain M90T))
Explore A0A4P7TTK5 
Go to UniProtKB:  A0A4P7TTK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4P7TTK5
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 RNF213B [auth C]67Homo 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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.220 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.609α = 90
b = 68.609β = 90
c = 147.694γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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