9I1I | pdb_00009i1i

Cryo-EM structure of mouse RNF213 (WB3/WB4 + ATP)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213.

Ahel, J., Balci, A., Faas, V., Grabarczyk, D.B., Harmo, R., Squair, D.R., Zhang, J., Roitinger, E., Lamoliatte, F., Mathur, S., Deszcz, L., Bell, L.E., Lehner, A., Williams, T.L., Sowar, H., Meinhart, A., Wood, N.T., Clausen, T., Virdee, S., Fletcher, A.J.

(2025) Nat Commun 16: 4414-4414

  • DOI: https://doi.org/10.1038/s41467-025-59444-4
  • Primary Citation Related Structures: 
    9I1I, 9I1J

  • PubMed Abstract: 

    The giant E3 ubiquitin ligase RNF213 is a conserved component of mammalian cell-autonomous immunity, limiting the replication of bacteria, viruses and parasites. To understand how RNF213 reacts to these unrelated pathogens, we employ chemical and structural biology to find that ATP binding to its ATPases Associated with diverse cellular Activities (AAA) core activates its E3 function. We develop methodology for proteome-wide E3 activity profiling inside living cells, revealing that RNF213 undergoes a reversible switch in E3 activity in response to cellular ATP abundance. Interferon stimulation of macrophages raises intracellular ATP levels and primes RNF213 E3 activity, while glycolysis inhibition depletes ATP and downregulates E3 activity. These data imply that ATP bears hallmarks of a danger/pathogen associated molecular pattern, coordinating cell-autonomous defence. Furthermore, quantitative labelling of RNF213 with E3-activity probes enabled us to identify the catalytic cysteine required for substrate ubiquitination and obtain a cryo-EM structure of the RNF213-E2-ubiquitin conjugation enzyme transfer intermediate, illuminating an unannotated E2 docking site. Together, our data demonstrate that RNF213 represents a new class of ATP-dependent E3 enzyme, employing distinct catalytic and regulatory mechanisms adapted to its specialised role in the broad defence against intracellular pathogens.

    • Organizational Affiliation: 
    • Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria.

Macromolecule Content 

  • Total Structure Weight: 587.71 kDa 
  • Atom Count: 36,852 
  • Modeled Residue Count: 4,584 
  • Deposited Residue Count: 5,161 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF2135,161Mus musculusMutation(s): 2 
Gene Names: Rnf213, Mystr
EC: 2.3.2.27 (PDB Primary Data), 3.6.4 (PDB Primary Data), 2.3.2 (PDB Primary Data)
UniProt
Find proteins for E9Q555 (Mus musculus)
Explore E9Q555 
Go to UniProtKB:  E9Q555
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9Q555
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Austrian Research Promotion AgencyAustria852936

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release