4AYC

RNF8 RING domain structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report



Literature

Rnf168 Ubiquitinates K13-15 on H2A/H2Ax to Drive DNA Damage Signaling

Mattiroli, F.Vissers, J.H.A.Van Dijk, W.J.Ikpa, P.Citterio, E.Vermeulen, W.Marteijn, J.A.Sixma, T.K.

(2012) Cell 150: 1182

  • DOI: 10.1016/j.cell.2012.08.005
  • Primary Citation of Related Structures:  
    4AYC

  • PubMed Abstract: 
  • Ubiquitin-dependent signaling during the DNA damage response (DDR) to double-strand breaks (DSBs) is initiated by two E3 ligases, RNF8 and RNF168, targeting histone H2A and H2AX. RNF8 is the first ligase recruited to the damage site, and RNF168 follows R ...

    Ubiquitin-dependent signaling during the DNA damage response (DDR) to double-strand breaks (DSBs) is initiated by two E3 ligases, RNF8 and RNF168, targeting histone H2A and H2AX. RNF8 is the first ligase recruited to the damage site, and RNF168 follows RNF8-dependent ubiquitination. This suggests that RNF8 initiates H2A/H2AX ubiquitination with K63-linked ubiquitin chains and RNF168 extends them. Here, we show that RNF8 is inactive toward nucleosomal H2A, whereas RNF168 catalyzes the monoubiquitination of the histones specifically on K13-15. Structure-based mutagenesis of RNF8 and RNF168 RING domains shows that a charged residue determines whether nucleosomal proteins are recognized. We find that K63 ubiquitin chains are conjugated to RNF168-dependent H2A/H2AX monoubiquitination at K13-15 and not on K118-119. Using a mutant of RNF168 unable to target histones but still catalyzing ubiquitin chains at DSBs, we show that ubiquitin chains per se are insufficient for signaling, but RNF168 target ubiquitination is required for DDR.


    Organizational Affiliation

    Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE RNF8 A138Homo sapiensMutation(s): 0 
Gene Names: RNF8KIAA0646
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for O76064 (Homo sapiens)
Explore O76064 
Go to UniProtKB:  O76064
NIH Common Fund Data Resources
PHAROS:  O76064
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE RNF8 B138Homo sapiensMutation(s): 0 
Gene Names: RNF8KIAA0646
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for O76064 (Homo sapiens)
Explore O76064 
Go to UniProtKB:  O76064
NIH Common Fund Data Resources
PHAROS:  O76064
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.374α = 90
b = 213.717β = 90
c = 34.102γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-26
    Type: Initial release