4DL3

Human DNA polymerase eta inserting dCMPNPP opposite GG template (GG0b).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta

Zhao, Y.Biertumpfel, C.Gregory, M.T.Hua, Y.J.Hanaoka, F.Yang, W.

(2012) Proc Natl Acad Sci U S A 109: 7269-7274

  • DOI: 10.1073/pnas.1202681109
  • Primary Citation of Related Structures:  
    4DL4, 4DL5, 4DL6, 4DL7, 4DL2, 4DL3

  • PubMed Abstract: 
  • Cisplatin (cis-diamminedichloroplatinum) and related compounds cause DNA damage and are widely used as anticancer agents. Chemoresistance to cisplatin treatment is due in part to translesion synthesis by human DNA polymerase η (hPol η). Here, we report crystal structures of hPol η complexed with intrastrand cisplatin-1,2-cross-linked DNA, representing four consecutive steps in translesion synthesis ...

    Cisplatin (cis-diamminedichloroplatinum) and related compounds cause DNA damage and are widely used as anticancer agents. Chemoresistance to cisplatin treatment is due in part to translesion synthesis by human DNA polymerase η (hPol η). Here, we report crystal structures of hPol η complexed with intrastrand cisplatin-1,2-cross-linked DNA, representing four consecutive steps in translesion synthesis. In contrast to the generally enlarged and nondiscriminating active site of Y-family polymerases like Dpo4, Pol η is specialized for efficient bypass of UV-cross-linked pyrimidine dimers. Human Pol η differs from the yeast homolog in its binding of DNA template. To incorporate deoxycytidine opposite cisplatin-cross-linked guanines, hPol η undergoes a specific backbone rearrangement to accommodate the larger base dimer and minimizes the DNA distortion around the lesion. Our structural analyses show why Pol η is inefficient at extending primers after cisplatin lesions, which necessitates a second translesion DNA polymerase to complete bypass in vivo. A hydrophobic pocket near the primer-binding site in human Pol η is identified as a potential drug target for inhibiting translesion synthesis and, thereby, reducing chemoresistance.


    Organizational Affiliation

    Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase eta A435Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*AP*CP*GP*GP*TP*CP*AP*CP*AP*CP*T)-3')T12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*C)-3')P9N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      0KX
      Query on 0KX

      Download Ideal Coordinates CCD File 
      P
      2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
      C9 H17 N4 O12 P3
      STYMTWKSQLVXJN-SHYZEUOFSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      A
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       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: 2.10 Å
      • R-Value Free: 0.217 
      • R-Value Work: 0.204 
      • R-Value Observed: 0.205 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 97.38α = 90
      b = 97.38β = 90
      c = 81γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      XDSdata reduction
      XSCALEdata scaling
      PHENIXphasing

      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: 2013-06-26
        Changes: Database references