4FVM | pdb_00004fvm

Crystal structure of yeast DNA polymerase alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha

Perera, R.L.Torella, R.Klinge, S.Kilkenny, M.L.Maman, J.D.Pellegrini, L.

(2013) Elife 2: e00482

  • DOI: https://doi.org/10.7554/eLife.00482
  • Primary Citation Related Structures: 
    4B08, 4FVM, 4FXD, 4FYD

  • PubMed Abstract: 

    The DNA Polymerase α (Pol α)/primase complex initiates DNA synthesis in eukaryotic replication. In the complex, Pol α and primase cooperate in the production of RNA-DNA oligonucleotides that prime synthesis of new DNA. Here we report crystal structures of the catalytic core of yeast Pol α in unliganded form, bound to an RNA primer/DNA template and extending an RNA primer with deoxynucleotides. We combine the structural analysis with biochemical and computational data to demonstrate that Pol α specifically recognizes the A-form RNA/DNA helix and that the ensuing synthesis of B-form DNA terminates primer synthesis. The spontaneous release of the completed RNA-DNA primer by the Pol α/primase complex simplifies current models of primer transfer to leading- and lagging strand polymerases. The proposed mechanism of nucleotide polymerization by Pol α might contribute to genomic stability by limiting the amount of inaccurate DNA to be corrected at the start of each Okazaki fragment. DOI:http://dx.doi.org/10.7554/eLife.00482.001.


  • Organizational Affiliation
    • Department of Biochemistry , University of Cambridge , Cambridge , United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 103.53 kDa 
  • Atom Count: 6,899 
  • Modeled Residue Count: 829 
  • Deposited Residue Count: 910 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit A910Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC17N2181POL1YNL102W
EC: 2.7.7.7
UniProt
Find proteins for P13382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13382 
Go to UniProtKB:  P13382
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13382
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.38α = 90
b = 127.14β = 104.78
c = 74.57γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-24
    Changes: Database references
  • Version 1.2: 2014-01-15
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description