3NG2 | pdb_00003ng2

Crystal structure of the RNF4 ring domain dimer

• PDB DOI: https://doi.org/10.2210/pdb3NG2/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-10 Released: 2010-10-06 
• Deposition Author(s): Liew, C.W., Day, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.242 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

RING domain dimerization is essential for RNF4 function

Liew, C.W., Sun, H., Hunter, T., Day, C.L.

(2010) Biochem J 431: 23-29

• PubMed: 20681948 
• DOI: https://doi.org/10.1042/BJ20100957
• Primary Citation Related Structures: 
  3NG2


• PubMed Abstract: 
  

  RNF4 [RING (really interesting new gene) finger protein 4] family ubiquitin ligases are RING E3 ligases that regulate the homoeostasis of SUMOylated proteins by promoting their ubiquitylation. In the present paper we report that the RING domain of RNF4 forms a stable dimer, and that dimerization is required for ubiquitin transfer. Our results suggest that the stability of the E2~ubiquitin thioester bond is regulated by RING domain dimerization.

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Organizational Affiliation: 
• Biochemistry Department, University of Otago, Dunedin 9054, New Zealand.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.13 kDa 
• Atom Count: 1,090 
• Modeled Residue Count: 133 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RING finger protein 4	A, B	71	Rattus norvegicus	Mutation(s): 0  Gene Names: Rnf4 EC: 2.3.2.27
UniProt
Find proteins for O88846 (Rattus norvegicus) Explore O88846  Go to UniProtKB:  O88846

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.242 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.487	α = 90
b = 85.922	β = 90
c = 22.277	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Liew, C.W., Day, C.L.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description