7OIK | pdb_00007oik

Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized

• PDB DOI: https://doi.org/10.2210/pdb7OIK/pdb
• EM Map EMD-12931: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-11 Released: 2022-06-01 
• Deposition Author(s): Grabarczyk, D., Ahel, J., Clausen, T.
• Funding Organization(s): European Research Council (ERC), Austrian Research Promotion Agency, Medical Research Council (MRC, United Kingdom), Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP

Ahel, J., Fletcher, A.J., Grabarczyk, D., Roitinger, E., Deszcz, L., Lehner, A., Virdee, S., Clausen, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 606.41 kDa 
• Atom Count: 36,779 
• Modeled Residue Count: 4,579 
• Deposited Residue Count: 5,327 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF213	A	5,161	Mus musculus	Mutation(s): 0  Gene Names: Rnf213, Mystr EC: 2.3.2.27 (PDB Primary Data), 3.6.4 (PDB Primary Data), 2.3.2 (UniProt)
UniProt
Find proteins for E9Q555 (Mus musculus) Explore E9Q555  Go to UniProtKB:  E9Q555

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 L3	B	166	Homo sapiens	Mutation(s): 0  Gene Names: UBE2L3, UBCE7, UBCH7 EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P68036 (Homo sapiens) Explore P68036  Go to UniProtKB:  P68036
PHAROS:  P68036 GTEx:  ENSG00000185651

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Grabarczyk, D., Ahel, J., Clausen, T.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	Austria	694978
Austrian Research Promotion Agency	Austria	852936
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UU_12016/8
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/ P003982/1

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Refinement description, Structure summary