4GB0

Crystal Structure of the RING domain of RNF168

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report



Literature

Structural basis for role of ring finger protein RNF168 RING domain

Zhang, X.Q., Chen, J., Wu, M., Wu, H., Arokiaraj, A.W., Wang, C.L., Zhang, W., Tao, Y., Huen, M.S., Zang, J.Y.

(2013) Cell Cycle 12: 312-321

  • DOI: 10.4161/cc.23104
  • Primary Citation of Related Structures:  
    4GB0

  • PubMed Abstract: 

    • Ubiquitin adducts surrounding DNA double-strand breaks (DSBs) have emerged as molecular platforms important for the assembly of DNA damage mediator and repair proteins. Central to these chromatin modifications lies the E2 UBC13, which has been implicated ...

    Ubiquitin adducts surrounding DNA double-strand breaks (DSBs) have emerged as molecular platforms important for the assembly of DNA damage mediator and repair proteins. Central to these chromatin modifications lies the E2 UBC13, which has been implicated in a bipartite role in priming and amplifying lys63-linked ubiquitin chains on histone molecules through coupling with the E3 RNF8 and RNF168. However, unlike the RNF8-UBC13 holoenyzme, exactly how RNF168 work in concert with UBC13 remains obscure. To provide a structural perspective for the RNF168-UBC13 complex, we solved the crystal structure of the RNF168 RING domain. Interestingly, while the RNF168 RING adopts a typical RING finger fold with two zinc ions coordinated by several conserved cystine and histine residues arranged in a C3HC4 "cross-brace" manner, structural superimposition of RNF168 RING with other UBC13-binding E3 ubiquitin ligases revealed substantial differences at its corresponding UBC13-binding interface. Consistently, and in stark contrast to that between RNF8 and UBC13, RNF168 did not stably associate with UBC13 in vitro or in vivo. Moreover, domain-swapping experiments indicated that the RNF8 and RNF168 RING domains are not functionally interchangeable. We propose that RNF8 and RNF168 operate in different modes with their cognate E2 UBC13 at DSBs.

    Organizational Affiliation: 

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, People's Republic of China.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF168 A121Homo sapiensMutation(s): 0 
Gene Names: RNF168
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q8IYW5 (Homo sapiens)
Explore Q8IYW5 
Go to UniProtKB:  Q8IYW5
NIH Common Fund Data Resources
PHAROS:  Q8IYW5
GTEx:  ENSG00000163961
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI
Download Ideal Coordinates CCD File 
A
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.16α = 90
b = 50.16β = 90
c = 113.93γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AutoSolphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release