4A09

Structure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at D-1 position) at 3.1 A resolution (CPD 2)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

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

Scrima, A., Fischer, E.S., Iwai, S., Gut, H., 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 provide the molecular basis for DDB2 receptor-mediated cyclobutane pyrimidine dimer recognition in chromatin ...

    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

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA DAMAGE-BINDING PROTEIN 1 A1159Homo sapiensMutation(s): 1 
Gene Names: DDB1, XAP1
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
NIH Common Fund Data Resources
PHAROS:  Q16531
GTEx:  ENSG00000167986
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA DAMAGE-BINDING PROTEIN 2 B382Danio rerioMutation(s): 2 
Gene Names: ddb2, si:dkey-45f10.3
Find proteins for Q2YDS1 (Danio rerio)
Explore Q2YDS1 
Go to UniProtKB:  Q2YDS1
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*GP)-3'G14synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3'H16synthetic construct
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CA
      Query on CA
      Download Ideal Coordinates CCD File 
      B
      		CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.10 Å
      • R-Value Free: 0.308 
      • R-Value Work: 0.245 
      • R-Value Observed: 0.248 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 111.65α = 90
      b = 122.94β = 90
      c = 154.2γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      XSCALEdata scaling
      PHASERphasing

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2011-11-30
        Type: Initial release
      • Version 1.1: 2011-12-07
        Changes: Database references
      • Version 1.2: 2019-04-03
        Changes: Data collection, Derived calculations, Other, Source and taxonomy