4ORH

Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.802 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation.

Campbell, S.J.Edwards, R.A.Leung, C.C.Neculai, D.Hodge, C.D.Dhe-Paganon, S.Glover, J.N.

(2012) J.Biol.Chem. 287: 23900-23910

  • DOI: 10.1074/jbc.M112.359653
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The repair of DNA double strand breaks by homologous recombination relies on the unique topology of the chains formed by Lys-63 ubiquitylation of chromatin to recruit repair factors such as breast cancer 1 (BRCA1) to sites of DNA damage. The human RI ...

    The repair of DNA double strand breaks by homologous recombination relies on the unique topology of the chains formed by Lys-63 ubiquitylation of chromatin to recruit repair factors such as breast cancer 1 (BRCA1) to sites of DNA damage. The human RING finger (RNF) E3 ubiquitin ligases, RNF8 and RNF168, with the E2 ubiquitin-conjugating complex Ubc13/Mms2, perform the majority of Lys-63 ubiquitylation in homologous recombination. Here, we show that RNF8 dimerizes and binds to Ubc13/Mms2, thereby stimulating formation of Lys-63 ubiquitin chains, whereas the related RNF168 RING domain is a monomer and does not catalyze Lys-63 polyubiquitylation. The crystal structure of the RNF8/Ubc13/Mms2 ternary complex reveals the structural basis for the interaction between Ubc13 and the RNF8 RING and that an extended RNF8 coiled-coil is responsible for its dimerization. Mutations that disrupt the RNF8/Ubc13 binding surfaces, or that truncate the RNF8 coiled-coil, reduce RNF8-catalyzed ubiquitylation. These findings support the hypothesis that RNF8 is responsible for the initiation of Lys-63-linked ubiquitylation in the DNA damage response, which is subsequently amplified by RNF168.


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 variant 2
A, E, I
153Homo sapiensMutation(s): 0 
Gene Names: UBE2V2 (MMS2, UEV2)
Find proteins for Q15819 (Homo sapiens)
Go to Gene View: UBE2V2
Go to UniProtKB:  Q15819
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
B, F, J
160Homo sapiensMutation(s): 0 
Gene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF8
C, G, H, K, L
149Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C, G, H, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.802 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.276 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 205.258α = 90.00
b = 205.258β = 90.00
c = 235.372γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
PHASERphasing
PHENIXrefinement
Blu-Icedata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-11-05
    Type: Structure summary
  • Version 1.2: 2014-12-03
    Type: Structure summary
  • Version 1.3: 2017-11-22
    Type: Refinement description