8S24 | pdb_00008s24

Structure of the E3 ubiquitin ligase RNF213, determined by cryoEM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213.

Crespillo-Casado, A.Pothukuchi, P.Naydenova, K.Yip, M.C.J.Young, J.M.Boulanger, J.Dharamdasani, V.Harper, C.Hammoudi, P.M.Otten, E.G.Boyle, K.Gogoi, M.Malik, H.S.Randow, F.

(2024) EMBO Rep 25: 4979-5005

  • DOI: https://doi.org/10.1038/s44319-024-00280-w
  • Primary Citation of Related Structures:  
    8S24

  • PubMed Abstract: 

    Innate immunity senses microbial ligands known as pathogen-associated molecular patterns (PAMPs). Except for nucleic acids, PAMPs are exceedingly taxa-specific, thus enabling pattern recognition receptors to detect cognate pathogens while ignoring others. How the E3 ubiquitin ligase RNF213 can respond to phylogenetically distant pathogens, including Gram-negative Salmonella, Gram-positive Listeria, and eukaryotic Toxoplasma, remains unknown. Here we report that the evolutionary history of RNF213 is indicative of repeated adaptation to diverse pathogen target structures, especially in and around its newly identified CBM20 carbohydrate-binding domain, which we have resolved by cryo-EM. We find that RNF213 forms coats on phylogenetically distant pathogens. ATP hydrolysis by RNF213's dynein-like domain is essential for coat formation on all three pathogens studied as is RZ finger-mediated E3 ligase activity for bacteria. Coat formation is not diffusion-limited but instead relies on rate-limiting initiation events and subsequent cooperative incorporation of further RNF213 molecules. We conclude that RNF213 responds to evolutionarily distant pathogens through enzymatically amplified cooperative recruitment.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF2135,247Homo sapiensMutation(s): 1 
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: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references