6T7Y

Structure of PCNA bound to cPIP motif of DP2 from P. abyssi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA.

Madru, C.Henneke, G.Raia, P.Hugonneau-Beaufet, I.Pehau-Arnaudet, G.England, P.Lindahl, E.Delarue, M.Carroni, M.Sauguet, L.

(2020) Nat Commun 11: 1591-1591

  • DOI: https://doi.org/10.1038/s41467-020-15392-9
  • Primary Citation of Related Structures:  
    6T7X, 6T7Y, 6T8H

  • PubMed Abstract: 

    Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD-PCNA complex from Pyrococcus abyssi at 3.77 Å. Using an integrative structural biology approach - combining cryo-EM, X-ray crystallography, protein-protein interaction measurements, and activity assays - we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Polα replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication.


  • Organizational Affiliation

    Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase sliding clamp261Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: pcnPYRAB13790PAB1465
UniProt
Find proteins for Q9UYX8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9UYX8 
Go to UniProtKB:  Q9UYX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UYX8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cPIP motif from the DP2 large subunit of PolD12Pyrococcus abyssiMutation(s): 0 
EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (UniProt)
UniProt
Find proteins for Q9V2F4 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2F4 
Go to UniProtKB:  Q9V2F4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V2F4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.193 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.736α = 90
b = 140.736β = 90
c = 38.521γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-17-CE11-0005-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2020-04-08
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description