3E0J

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta.

Baranovskiy, A.G.Babayeva, N.D.Liston, V.G.Rogozin, I.B.Koonin, E.V.Pavlov, Y.I.Vassylyev, D.G.Tahirov, T.H.

(2008) Cell Cycle 7: 3026-3036

  • DOI: 10.4161/cc.7.19.6720

  • PubMed Abstract: 
  • The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance. Regulation of the plethora of Pol delta functions depends on the interaction between the second (p50) and t ...

    The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance. Regulation of the plethora of Pol delta functions depends on the interaction between the second (p50) and third (p66) non-catalytic subunits. We report the crystal structure of p50*p66(N) complex featuring oligonucleotide binding and phosphodiesterase domains in p50 and winged helix-turn-helix N-terminal domain in p66. Disruption of the interaction between the yeast orthologs of p50 and p66 by strategic amino acid changes leads to cold-sensitivity, sensitivity to hydroxyurea and to reduced UV mutagenesis, mimicking the phenotypes of strains where the third subunit of Pol delta is absent. The second subunits of all B family replicative DNA polymerases in archaea and eukaryotes, except Pol delta, share a three-domain structure similar to p50*p66(N), raising the possibility that a portion of the gene encoding p66 was derived from the second subunit gene relatively late in evolution.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of the complex of the second and third regulatory subunits of human Pol delta.
      Baranovskiy, A.G.,Babayeva, N.D.,Pavlov, Y.I.,Tahirov, T.H.
      (2008) Acta Crystallogr.,Sect.F 64: 822


    Organizational Affiliation

    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-7696, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase subunit delta-2
A, C, E, G
476Homo sapiensMutation(s): 0 
Gene Names: POLD2
Find proteins for P49005 (Homo sapiens)
Go to Gene View: POLD2
Go to UniProtKB:  P49005
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase subunit delta-3
B, D, F, H
144Homo sapiensMutation(s): 0 
Gene Names: POLD3 (KIAA0039)
Find proteins for Q15054 (Homo sapiens)
Go to Gene View: POLD3
Go to UniProtKB:  Q15054
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.257 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.128α = 90.00
b = 248.535β = 106.94
c = 103.461γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
DMphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance