3E0J

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  
    3E0J

  • 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 third (p66) non-catalytic subunits ...

    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 Struct Biol Cryst Commun 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase subunit delta-2 A, C, E, G476Homo sapiensMutation(s): 0 
Gene Names: POLD2
EC: 2.7.7.7
Find proteins for P49005 (Homo sapiens)
Explore P49005 
Go to UniProtKB:  P49005
NIH Common Fund Data Resources
PHAROS:  P49005
GTEx:  ENSG00000106628
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase subunit delta-3 B, D, F, H144Homo sapiensMutation(s): 0 
Gene Names: POLD3, KIAA0039
Find proteins for Q15054 (Homo sapiens)
Explore Q15054 
Go to UniProtKB:  Q15054
NIH Common Fund Data Resources
PHAROS:  Q15054
GTEx:  ENSG00000077514
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.128α = 90
b = 248.535β = 106.94
c = 103.461γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-10-21
    Changes: Data collection, Database references