4A0K

STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.93 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation.

Fischer, E.S.Scrima, A.Bohm, K.Matsumoto, S.Lingaraju, G.M.Faty, M.Yasuda, T.Cavadini, S.Wakasugi, M.Hanaoka, F.Iwai, S.Gut, H.Sugasawa, K.Thoma, N.H.

(2011) Cell 147: 1024

  • DOI: 10.1016/j.cell.2011.10.035
  • Primary Citation of Related Structures:  
    4A0A, 4A0B, 4A08, 4A09, 4A0K, 4A0L, 4A11, 4A0C

  • PubMed Abstract: 
  • The DDB1-CUL4-RBX1 (CRL4) ubiquitin ligase family regulates a diverse set of cellular pathways through dedicated substrate receptors (DCAFs). The DCAF DDB2 detects UV-induced pyrimidine dimers in the genome and facilitates nucleotide excision repair. We ...

    The DDB1-CUL4-RBX1 (CRL4) ubiquitin ligase family regulates a diverse set of cellular pathways through dedicated substrate receptors (DCAFs). The DCAF DDB2 detects UV-induced pyrimidine dimers in the genome and facilitates nucleotide excision repair. We provide the molecular basis for DDB2 receptor-mediated cyclobutane pyrimidine dimer recognition in chromatin. The structures of the fully assembled DDB1-DDB2-CUL4A/B-RBX1 (CRL4(DDB2)) ligases reveal that the mobility of the ligase arm creates a defined ubiquitination zone around the damage, which precludes direct ligase activation by DNA lesions. Instead, the COP9 signalosome (CSN) mediates the CRL4(DDB2) inhibition in a CSN5 independent, nonenzymatic, fashion. In turn, CSN inhibition is relieved upon DNA damage binding to the DDB2 module within CSN-CRL4(DDB2). The Cockayne syndrome A DCAF complex crystal structure shows that CRL4(DCAF(WD40)) ligases share common architectural features. Our data support a general mechanism of ligase activation, which is induced by CSN displacement from CRL4(DCAF) on substrate binding to the DCAF.


    Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CULLIN-4A A742Homo sapiensMutation(s): 0 
Gene Names: CUL4A
Find proteins for Q13619 (Homo sapiens)
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Go to UniProtKB:  Q13619
NIH Common Fund Data Resources
PHAROS:  Q13619
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE RBX1 B117Mus musculusMutation(s): 0 
Gene Names: Rbx1
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt), 2.3.2.32 (UniProt)
Find proteins for P62878 (Mus musculus)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA DAMAGE-BINDING PROTEIN 1 C1159Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
Find proteins for Q16531 (Homo sapiens)
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Go to UniProtKB:  Q16531
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PHAROS:  Q16531
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA DAMAGE-BINDING PROTEIN 2 D382Danio rerioMutation(s): 2 
Gene Names: ddb2si:dkey-45f10.3
Find proteins for Q2YDS1 (Danio rerio)
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Go to UniProtKB:  Q2YDS1
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 5
    MoleculeChainsLengthOrganismImage
    12 BP THF CONTAINING DNAE12synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 6
      MoleculeChainsLengthOrganismImage
      12 BP DNAF12synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 5.93 Å
      • R-Value Free: 0.270 
      • R-Value Work: 0.269 
      • R-Value Observed: 0.269 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 210.65α = 90
      b = 78.02β = 108.5
      c = 276.62γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      XDSdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2011-12-14
        Type: Initial release
      • Version 1.1: 2019-04-03
        Changes: Data collection, Derived calculations, Other, Source and taxonomy