9F26 | pdb_00009f26

Crystal structure of the PriS_PriL-Rpa2WH ternary complex from P. abyssi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.256 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Communication between DNA polymerases and Replication Protein A within the archaeal replisome.

Martinez-Carranza, M.Vialle, L.Madru, C.Cordier, F.Tekpinar, A.D.Haouz, A.Legrand, P.Le Meur, R.A.England, P.Dulermo, R.Guijarro, J.I.Henneke, G.Sauguet, L.

(2024) Nat Commun 15: 10926-10926

  • DOI: https://doi.org/10.1038/s41467-024-55365-w
  • Primary Citation of Related Structures:  
    9F26, 9F27, 9F28, 9F29, 9F2A

  • PubMed Abstract: 

    Replication Protein A (RPA) plays a pivotal role in DNA replication by coating and protecting exposed single-stranded DNA, and acting as a molecular hub that recruits additional replication factors. We demonstrate that archaeal RPA hosts a winged-helix domain (WH) that interacts with two key actors of the replisome: the DNA primase (PriSL) and the replicative DNA polymerase (PolD). Using an integrative structural biology approach, combining nuclear magnetic resonance, X-ray crystallography and cryo-electron microscopy, we unveil how RPA interacts with PriSL and PolD through two distinct surfaces of the WH domain: an evolutionarily conserved interface and a novel binding site. Finally, RPA is shown to stimulate the activity of PriSL in a WH-dependent manner. This study provides a molecular understanding of the WH-mediated regulatory activity in central replication factors such as RPA, which regulate genome maintenance in Archaea and Eukaryotes.


  • Organizational Affiliation
    • Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunit PriS346Pyrococcus abyssiMutation(s): 0 
Gene Names: priSpriAPYRAB01820PAB2236
EC: 2.7.7
UniProt
Find proteins for Q9V292 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V292 
Go to UniProtKB:  Q9V292
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V292
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunit PriL393Pyrococcus abyssiMutation(s): 0 
Gene Names: priLpriBPYRAB01830PAB2235
UniProt
Find proteins for Q9V291 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V291 
Go to UniProtKB:  Q9V291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V291
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination272Pyrococcus abyssiMutation(s): 0 
Gene Names: PAB2165
UniProt
Find proteins for Q9V1Z1 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V1Z1 
Go to UniProtKB:  Q9V1Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V1Z1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.256 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.815α = 90
b = 101.505β = 90
c = 177.805γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceARCHAPRIM
Fondation pour la Recherche Medicale (FRM)France--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references