4WHV

E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.30 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.329 
  • R-Value Observed: 0.330 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment.

Hodge, C.D., Ismail, I.H., Edwards, R.A., Hura, G.L., Xiao, A.T., Tainer, J.A., Hendzel, M.J., Glover, J.N.

(2016) J Biol Chem 291: 9396-9410

  • DOI: 10.1074/jbc.M116.715698
  • Primary Citation of Related Structures:  
    4WHV

  • PubMed Abstract: 

    • DNA double strand break (DSB) responses depend on the sequential actions of the E3 ubiquitin ligases RNF8 and RNF168 plus E2 ubiquitin-conjugating enzyme Ubc13 to specifically generate histone Lys-63-linked ubiquitin chains in DSB signaling. Here, we def ...

    DNA double strand break (DSB) responses depend on the sequential actions of the E3 ubiquitin ligases RNF8 and RNF168 plus E2 ubiquitin-conjugating enzyme Ubc13 to specifically generate histone Lys-63-linked ubiquitin chains in DSB signaling. Here, we defined the activated RNF8-Ubc13∼ubiquitin complex by x-ray crystallography and its functional solution conformations by x-ray scattering, as tested by separation-of-function mutations imaged in cells by immunofluorescence. The collective results show that the RING E3 RNF8 targets E2 Ubc13 to DSB sites and plays a critical role in damage signaling by stimulating polyubiquitination through modulating conformations of ubiquitin covalently linked to the Ubc13 active site. Structure-guided separation-of-function mutations show that the RNF8 E2 stimulating activity is essential for DSB signaling in mammalian cells and is necessary for downstream recruitment of 53BP1 and BRCA1. Chromatin-targeted RNF168 rescues 53BP1 recruitment involved in non-homologous end joining but not BRCA1 recruitment for homologous recombination. These findings suggest an allosteric approach to targeting the ubiquitin-docking cleft at the E2-E3 interface for possible interventions in cancer and chronic inflammation, and moreover, they establish an independent RNF8 role in BRCA1 recruitment.

    Organizational Affiliation: 

    From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada, mark.glover@ualberta.ca.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 N B, E, H, K160Homo sapiensMutation(s): 1 
Gene Names: UBE2N, BLU
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS:  P61088
GTEx:  ENSG00000177889
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF8 C, D, I, J149Homo sapiensMutation(s): 0 
Gene Names: RNF8, KIAA0646
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
GTEx:  ENSG00000112130
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B A, F, G, L83Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.30 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.329 
  • R-Value Observed: 0.330 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 341.379α = 90
b = 341.379β = 90
c = 113.447γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2016-05-11
    Changes: Database references, Structure summary
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description