4AYC

RNF8 RING domain structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • 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 follo ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE RNF8
A
138Homo sapiensMutation(s): 0 
Gene Names: RNF8 (KIAA0646)
EC: 2.3.2.27
Find proteins for O76064 (Homo sapiens)
Go to Gene View: RNF8
Go to UniProtKB:  O76064
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE RNF8
B
138Homo sapiensMutation(s): 0 
Gene Names: RNF8 (KIAA0646)
EC: 2.3.2.27
Find proteins for O76064 (Homo sapiens)
Go to Gene View: RNF8
Go to UniProtKB:  O76064
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CPQ
Query on CPQ

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Download CCD File 
A
N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
DEOXY-BIGCHAP
C42 H75 N3 O15
OJSUWTDDXLCUFR-HGZMBBKESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.374α = 90.00
b = 213.717β = 90.00
c = 34.102γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SHELXDphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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