9F29 | pdb_00009f29

Pyrococcus abyssi PolD in complex with Rpa2 winged-helix domain class 1 (composite map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
RPA32 subunit of the hetero-oligomeric complex involved in homologous recombinationA [auth C]132Pyrococcus abyssi GE5Mutation(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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase II small subunitB [auth A]662Pyrococcus abyssi GE5Mutation(s): 1 
Gene Names: polB
EC: 2.7.7.7 (UniProt), 3.1.11.1 (UniProt)
UniProt
Find proteins for Q9V2F3 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2F3 
Go to UniProtKB:  Q9V2F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V2F3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase II large subunitC [auth B]1,270Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: polCPF0019
EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (PDB Primary Data)
UniProt
Find proteins for P81409 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore P81409 
Go to UniProtKB:  P81409
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81409
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--
Fondation pour la Recherche Medicale (FRM)France--
H2020 Marie Curie Actions of the European CommissionEuropean Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-09
    Changes: Data collection