8S24

Structure of the E3 ubiquitin ligase RNF213, determined by cryoEM

• PDB DOI: https://doi.org/10.2210/pdb8S24/pdb
• EM Map EMD-19653: EMDB EMDataResource

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-02-16 Released: 2024-10-09 
• Deposition Author(s): Naydenova, K., Randow, F.
• Funding Organization(s): UK Research and Innovation (UKRI), Wellcome Trust

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Experimental Data Snapshot

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

Starting Model: in silico

Literature

Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213

Casado, A.C., 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 J 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 597.05 kDa 
• Atom Count: 35,357 
• Modelled Residue Count: 4,387 
• Deposited Residue Count: 5,247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF213	A	5,247	Homo sapiens	Mutation(s): 1  Gene Names: RNF213, ALO17, C17orf27, KIAA1554, KIAA1618, MYSTR 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Naydenova, K., Randow, F.

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Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	U105170648
Wellcome Trust	United Kingdom	222503/Z/21/Z

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release