4PPE | pdb_00004ppe

human RNF4 RING domain

• PDB DOI: https://doi.org/10.2210/pdb4PPE/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-26 Released: 2014-03-26 
• Deposition Author(s): Perry, J.J., Arvai, A.S., Hitomi, C., Tainer, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response.

Groocock, L.M., Nie, M., Prudden, J., Moiani, D., Wang, T., Cheltsov, A., Rambo, R.P., Arvai, A.S., Hitomi, C., Tainer, J.A., Luger, K., Perry, J.J., Lazzerini-Denchi, E., Boddy, M.N.

(2014) EMBO Rep 15: 601-608

• PubMed: 24714598 
• DOI: https://doi.org/10.1002/embr.201338369
• Primary Citation Related Structures: 
  4PPE


• PubMed Abstract: 
  

  The post-translational modification of DNA repair and checkpoint proteins by ubiquitin and small ubiquitin-like modifier (SUMO) critically orchestrates the DNA damage response (DDR). The ubiquitin ligase RNF4 integrates signaling by SUMO and ubiquitin, through its selective recognition and ubiquitination of SUMO-modified proteins. Here, we define a key new determinant for target discrimination by RNF4, in addition to interaction with SUMO. We identify a nucleosome-targeting motif within the RNF4 RING domain that can bind DNA and thereby enables RNF4 to selectively ubiquitinate nucleosomal histones. Furthermore, RNF4 nucleosome-targeting is crucially required for the repair of TRF2-depleted dysfunctional telomeres by 53BP1-mediated non-homologous end joining.

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Organizational Affiliation: 
• Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.79 kDa 
• Atom Count: 1,112 
• Modeled Residue Count: 133 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF4	A, B	76	Homo sapiens	Mutation(s): 0  Gene Names: RES4-26, RNF4, SNURF EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P78317 (Homo sapiens) Explore P78317  Go to UniProtKB:  P78317
PHAROS:  P78317 GTEx:  ENSG00000063978

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.938	α = 90
b = 86.987	β = 90
c = 22.869	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Perry, J.J., Arvai, A.S., Hitomi, C., Tainer, J.A.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations