human RNF4 RING domain

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1002/embr.201338369
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF4
A, B
76Homo sapiensMutation(s): 0 
Gene Names: RES4-26RNF4SNURF
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P78317 (Homo sapiens)
Explore P78317 
Go to UniProtKB:  P78317
PHAROS:  P78317
GTEx:  ENSG00000063978 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78317
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.938α = 90
b = 86.987β = 90
c = 22.869γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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