4EEY

Crystal structure of human DNA polymerase eta in ternary complex with a cisplatin DNA adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for cisplatin DNA damage tolerance by human polymerase {eta} during cancer chemotherapy.

Ummat, A.Rechkoblit, O.Jain, R.Roy Choudhury, J.Johnson, R.E.Silverstein, T.D.Buku, A.Lone, S.Prakash, L.Prakash, S.Aggarwal, A.K.

(2012) Nat Struct Mol Biol 19: 628-632

  • DOI: 10.1038/nsmb.2295
  • Primary Citation of Related Structures:  
    4EEY

  • PubMed Abstract: 
  • A major clinical problem in the use of cisplatin to treat cancers is tumor resistance. DNA polymerase η (Pol-η) is a crucial polymerase that allows cancer cells to cope with the cisplatin-DNA adducts that are formed during chemotherapy. We present here a structure of human Pol-η inserting deoxycytidine triphosphate (dCTP) opposite a cisplatin intrastrand cross-link (PtGpG) ...

    A major clinical problem in the use of cisplatin to treat cancers is tumor resistance. DNA polymerase η (Pol-η) is a crucial polymerase that allows cancer cells to cope with the cisplatin-DNA adducts that are formed during chemotherapy. We present here a structure of human Pol-η inserting deoxycytidine triphosphate (dCTP) opposite a cisplatin intrastrand cross-link (PtGpG). We show that the specificity of human Pol-η for PtGpG derives from an active site that is open to permit Watson-Crick geometry of the nascent PtGpG-dCTP base pair and to accommodate the lesion without steric hindrance. This specificity is augmented by the residues Gln38 and Ser62, which interact with PtGpG, and Arg61, which interacts with the incoming dCTP. Collectively, the structure provides a basis for understanding how Pol-η in human cells can tolerate the DNA damage caused by cisplatin chemotherapy and offers a framework for the design of inhibitors in cancer therapy.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase eta A435Homo sapiensMutation(s): 1 
Gene Names: POLHRAD30RAD30AXPV
EC: 2.7.7.7
Find proteins for Q9Y253 (Homo sapiens)
Explore Q9Y253 
Go to UniProtKB:  Q9Y253
NIH Common Fund Data Resources
PHAROS:  Q9Y253
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*TP*TP*GP*GP*TP*CP*TP*CP*CP*TP*CP*C)-3'T13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*GP*GP*AP*GP*GP*AP*GP*A)-3'P9N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DCP
      Query on DCP

      Download Ideal Coordinates CCD File 
      A
      2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
      C9 H16 N3 O13 P3
      RGWHQCVHVJXOKC-SHYZEUOFSA-N
       Ligand Interaction
      CPT
      Query on CPT

      Download Ideal Coordinates CCD File 
      T
      Cisplatin
      Cl2 H6 N2 Pt
      LXZZYRPGZAFOLE-UHFFFAOYSA-L
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.32 Å
      • R-Value Free: 0.233 
      • R-Value Work: 0.178 
      • R-Value Observed: 0.182 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.5α = 90
      b = 98.5β = 90
      c = 82.603γ = 120
      Software Package:
      Software NamePurpose
      CBASSdata collection
      PHASERphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2012-05-09
        Type: Initial release
      • Version 1.1: 2013-06-19
        Changes: Database references