4ORH | pdb_00004orh

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 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.276 (Depositor), 0.281 (DCC) 
  • R-Value Observed: 
    0.277 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4ORH

This is version 1.4 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 Biological Chem 287: 23900-23910

  • DOI: https://doi.org/10.1074/jbc.M112.359653
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 194.21 kDa 
  • Atom Count: 11,524 
  • Modeled Residue Count: 1,513 
  • Deposited Residue Count: 1,684 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 variant 2A,
D [auth E],
H [auth I]
153Homo sapiensMutation(s): 0 
Gene Names: MMS2UBE2V2UEV2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15819 (Homo sapiens)
Explore Q15819 
Go to UniProtKB:  Q15819
PHAROS:  Q15819
GTEx:  ENSG00000169139 
Entity Groups
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UniProt GroupQ15819
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 NB,
E [auth F],
I [auth J]
160Homo sapiensMutation(s): 0 
Gene Names: UBE2NBLU
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
PHAROS:  P61088
GTEx:  ENSG00000177889 
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UniProt GroupP61088
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF8C,
F [auth G],
G [auth H],
J [auth K],
K [auth L]
149Homo sapiensMutation(s): 0 
Gene Names: RNF8KIAA0646
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O76064 (Homo sapiens)
Explore O76064 
Go to UniProtKB:  O76064
PHAROS:  O76064
GTEx:  ENSG00000112130 
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UniProt GroupO76064
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
L [auth C]
M [auth C]
N [auth G]
O [auth G]
P [auth H]
L [auth C],
M [auth C],
N [auth G],
O [auth G],
P [auth H],
Q [auth H],
R [auth K],
S [auth K],
T [auth L],
U [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.80 Å
  • R-Value Free:  0.282 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.276 (Depositor), 0.281 (DCC) 
  • R-Value Observed: 0.277 (Depositor) 
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  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations