6ASR

REV1 UBM2 domain complex with ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structures of REV1 UBM2 Domain Complex with Ubiquitin and with a Small-Molecule that Inhibits the REV1 UBM2-Ubiquitin Interaction.

Vanarotti, M., Grace, C.R., Miller, D.J., Actis, M.L., Inoue, A., Evison, B.J., Vaithiyalingam, S., Singh, A.P., McDonald, E.T., Fujii, N.

(2018) J Mol Biol 430: 2857-2872

  • DOI: 10.1016/j.jmb.2018.05.042
  • Primary Citation of Related Structures:  
    6ASR, 6AXD

  • PubMed Abstract: 

    • REV1 is a DNA damage tolerance protein and encodes two ubiquitin-binding motifs (UBM1 and UBM2) that are essential for REV1 functions in cell survival under DNA-damaging stress. Here we report the first solution and X-ray crystal structures of REV1 UBM2 and its complex with ubiquitin, respectively ...

    REV1 is a DNA damage tolerance protein and encodes two ubiquitin-binding motifs (UBM1 and UBM2) that are essential for REV1 functions in cell survival under DNA-damaging stress. Here we report the first solution and X-ray crystal structures of REV1 UBM2 and its complex with ubiquitin, respectively. Furthermore, we have identified the first small-molecule compound, MLAF50, that directly binds to REV1 UBM2. In the heteronuclear single quantum coherence NMR experiments, peaks of UBM2 but not of UBM1 are significantly shifted by the addition of ubiquitin, which agrees to the observation that REV1 UBM2 but not UBM1 is required for DNA damage tolerance. REV1 UBM2 interacts with hydrophobic residues of ubiquitin such as L8 and L73. NMR data suggest that MLAF50 binds to the same residues of REV1 UBM2 that interact with ubiquitin, indicating that MLAF50 can compete with the REV1 UBM2-ubiquitin interaction orthosterically. Indeed, MLAF50 inhibited the interaction of REV1 UBM2 with ubiquitin and prevented chromatin localization of REV1 induced by cisplatin in U2OS cells. Our results structurally validate REV1 UBM2 as a target of a small-molecule inhibitor and demonstrate a new avenue to targeting ubiquitination-mediated protein interactions with a chemical tool.

    Organizational Affiliation: 

    Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. Electronic address: naoaki.fujii@gmail.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinA, C76Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein REV1B51Homo sapiensMutation(s): 0 
Gene Names: REV1, REV1L
EC: 2.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBZ9 (Homo sapiens)
Explore Q9UBZ9 
Go to UniProtKB:  Q9UBZ9
PHAROS:  Q9UBZ9
GTEx:  ENSG00000135945 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBZ9
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.924α = 90
b = 164.924β = 90
c = 164.924γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2017-08-25 
  • Released Date: 2018-06-20 
    • Deposition Author(s): Miller, D.J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references