4ORH

Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.277 

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:  
    3L11, 4ORH

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 variant 2AEI153Homo sapiensMutation(s): 0 
Gene Names: MMS2UBE2V2UEV2
Find proteins for Q15819 (Homo sapiens)
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Go to UniProtKB:  Q15819
NIH Common Fund Data Resources
PHAROS  Q15819
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NBFJ160Homo sapiensMutation(s): 0 
Gene Names: UBE2NBLU
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens)
Explore P61088 
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PHAROS  P61088
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF8CGHKL149Homo 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
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PHAROS  O76064
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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: 4.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.277 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.258α = 90
b = 205.258β = 90
c = 235.372γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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