3EI2

Structure of hsDDB1-drDDB2 bound to a 16 bp abasic site containing DNA-duplex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


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


Literature

Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.

Scrima, A., Konickova, R., Czyzewski, B.K., Kawasaki, Y., Jeffrey, P.D., Groisman, R., Nakatani, Y., Iwai, S., Pavletich, N.P., Thoma, N.H.

(2008) Cell 135: 1213-1223

  • DOI: 10.1016/j.cell.2008.10.045
  • Primary Citation of Related Structures:  
    3EI1, 3EI2, 3EI3, 3EI4

  • PubMed Abstract: 

    • Ultraviolet (UV) light-induced pyrimidine photodimers are repaired by the nucleotide excision repair pathway. Photolesions have biophysical parameters closely resembling undamaged DNA, impeding discovery through damage surveillance proteins. The DDB1-DDB ...

    Ultraviolet (UV) light-induced pyrimidine photodimers are repaired by the nucleotide excision repair pathway. Photolesions have biophysical parameters closely resembling undamaged DNA, impeding discovery through damage surveillance proteins. The DDB1-DDB2 complex serves in the initial detection of UV lesions in vivo. Here we present the structures of the DDB1-DDB2 complex alone and bound to DNA containing either a 6-4 pyrimidine-pyrimidone photodimer (6-4PP) lesion or an abasic site. The structure shows that the lesion is held exclusively by the WD40 domain of DDB2. A DDB2 hairpin inserts into the minor groove, extrudes the photodimer into a binding pocket, and kinks the duplex by approximately 40 degrees. The tightly localized probing of the photolesions, combined with proofreading in the photodimer pocket, enables DDB2 to detect lesions refractory to detection by other damage surveillance proteins. The structure provides insights into damage recognition in chromatin and suggests a mechanism by which the DDB1-associated CUL4 ubiquitin ligase targets proteins surrounding the site of damage.

    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 A1158Homo sapiensMutation(s): 0 
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 B383Danio rerioMutation(s): 0 
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(*DAP*DAP*DAP*DTP*DGP*DAP*DAP*DTP*(3DR)P*DAP*DAP*DGP*DCP*DAP*DGP*DG)-3'G16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      5'-D(*DCP*DCP*DTP*DGP*DCP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DTP*DT)-3'H16N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PG4
      Query on PG4
      Download Ideal Coordinates CCD File 
      A
      		TETRAETHYLENE GLYCOL
      C8 H18 O5
      UWHCKJMYHZGTIT-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.60 Å
      • R-Value Free: 0.268 
      • R-Value Work: 0.220 
      • R-Value Observed: 0.223 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 113.21α = 90
      b = 123.48β = 90
      c = 159.79γ = 90
      Software Package:
      Software NamePurpose
      XSCALEdata scaling
      MOLREPphasing
      REFMACrefinement
      PDB_EXTRACTdata extraction
      XDSdata scaling

      Structure Validation

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      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2009-01-20
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance