4Q8E

Human DNA polymerase eta inserting dCMPNPP opposite a phenanthriplatin adducted G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage.

Gregory, M.T.Park, G.Y.Johnstone, T.C.Lee, Y.S.Yang, W.Lippard, S.J.

(2014) Proc Natl Acad Sci U S A 111: 9133-9138

  • DOI: https://doi.org/10.1073/pnas.1405739111
  • Primary Citation of Related Structures:  
    4Q8E, 4Q8F

  • PubMed Abstract: 

    Platinum drugs are a mainstay of anticancer chemotherapy. Nevertheless, tumors often display inherent or acquired resistance to platinum-based treatments, prompting the search for new compounds that do not exhibit cross-resistance with current therapies. Phenanthriplatin, cis-diamminephenanthridinechloroplatinum(II), is a potent monofunctional platinum complex that displays a spectrum of activity distinct from those of the clinically approved platinum drugs. Inhibition of RNA polymerases by phenanthriplatin lesions has been implicated in its mechanism of action. The present study evaluates the ability of phenanthriplatin lesions to inhibit DNA replication, a function disrupted by traditional platinum drugs. Phenanthriplatin lesions effectively inhibit DNA polymerases ν, ζ, and κ and the Klenow fragment. In contrast to results obtained with DNA damaged by cisplatin, all of these polymerases were capable of inserting a base opposite a phenanthriplatin lesion, but only Pol η, an enzyme efficient in translesion synthesis, was able to fully bypass the adduct, albeit with low efficiency. X-ray structural characterization of Pol η complexed with site-specifically platinated DNA at both the insertion and +1 extension steps reveals that phenanthriplatin on DNA interacts with and inhibits Pol η in a manner distinct from that of cisplatin-DNA adducts. Unlike cisplatin and oxaliplatin, the efficacies of which are influenced by Pol η expression, phenanthriplatin is highly toxic to both Pol η+ and Pol η- cells. Given that increased expression of Pol η is a known mechanism by which cells resist cisplatin treatment, phenanthriplatin may be valuable in the treatment of cancers that are, or can easily become, resistant to cisplatin.


  • Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases andThe Johns Hopkins University-National Institutes of Health Graduate Partnership Program, National Institutes of Health, Bethesda, MD 20892; and.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase eta435Homo sapiensMutation(s): 0 
Gene Names: POLHPOLH RAD30 RAD30A XPVRAD30RAD30AXPV
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y253 (Homo sapiens)
Explore Q9Y253 
Go to UniProtKB:  Q9Y253
PHAROS:  Q9Y253
GTEx:  ENSG00000170734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y253
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*AP*TP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3'B [auth T]10N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3'C [auth P]8N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0KX
Query on 0KX

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

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.766α = 90
b = 98.766β = 90
c = 82.197γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2018-06-27
    Changes: Data collection, Derived calculations
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations