5XIS

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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Literature

Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.

Takahashi, T.S., Hirade, Y., Toma, A., Sato, Y., Yamagata, A., Goto-Ito, S., Tomita, A., Nakada, S., Fukai, S.

(2018) Nat Commun 9: 170-170

  • DOI: https://doi.org/10.1038/s41467-017-02345-y
  • Primary Citation of Related Structures:  
    5XIS, 5XIT, 5XIU, 5YDK

  • PubMed Abstract: 

    • The E3 ubiquitin (Ub) ligase RNF168 plays a critical role in the initiation of the DNA damage response to double-strand breaks (DSBs). The recruitment of RNF168 by ubiquitylated targets involves two distinct regions, Ub-dependent DSB recruitment module (UDM) 1 and UDM2 ...

    The E3 ubiquitin (Ub) ligase RNF168 plays a critical role in the initiation of the DNA damage response to double-strand breaks (DSBs). The recruitment of RNF168 by ubiquitylated targets involves two distinct regions, Ub-dependent DSB recruitment module (UDM) 1 and UDM2. Here we report the crystal structures of the complex between UDM1 and Lys63-linked diUb (K63-Ub 2 ) and that between the C-terminally truncated UDM2 (UDM2ΔC) and K63-Ub 2 . In both structures, UDM1 and UDM2ΔC fold as a single α-helix. Their simultaneous bindings to the distal and proximal Ub moieties provide specificity for Lys63-linked Ub chains. Structural and biochemical analyses of UDM1 elucidate an Ub-binding mechanism between UDM1 and polyubiquitylated targets. Mutations of Ub-interacting residues in UDM2 prevent the accumulation of RNF168 to DSB sites in U2OS cells, whereas those in UDM1 have little effect, suggesting that the interaction of UDM2 with ubiquitylated and polyubiquitylated targets mainly contributes to the RNF168 recruitment.

    Organizational Affiliation: 

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan. fukai@iam.u-tokyo.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF168A, D84Homo sapiensMutation(s): 0 
Gene Names: RNF168
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYW5 (Homo sapiens)
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Go to UniProtKB:  Q8IYW5
PHAROS:  Q8IYW5
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UniProt GroupQ8IYW5
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aB, E77Mus musculusMutation(s): 0 
Gene Names: Rps27a, Uba80, Ubcep1
UniProt
Find proteins for P62983 (Mus musculus)
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UniProt GroupP62983
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aC, F76Mus musculusMutation(s): 1 
Gene Names: Rps27a, Uba80, Ubcep1
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Find proteins for P62983 (Mus musculus)
Explore P62983 
Go to UniProtKB:  P62983
Entity Groups  
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UniProt GroupP62983
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYZ
Query on XYZ
Download Ideal Coordinates CCD File 
G [auth A],
J [auth D]		beta-D-xylofuranose
C5 H10 O5
HMFHBZSHGGEWLO-KKQCNMDGSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
H [auth B],
I [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.273α = 76.47
b = 66.291β = 79.29
c = 74.173γ = 80.49
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
JSPSJapan22121003
JSPSJapan15H01175
JSPSJapan24247014
JSPSJapan24687012
JSPSJapan16H04750
JSTJapanJPMJCR1XMX5
JSPSJapan15F15386

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary