9F2A | pdb_00009f2a

Pyrococcus abyssi PolD in complex with Rpa2 winged-helix domain class 2 (composite map)

• PDB DOI: https://doi.org/10.2210/pdb9F2A/pdb
• EM Map EMD-50143: EMDB EMDataResource

• Classification: REPLICATION
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-04-22 Released: 2024-12-04 
• Deposition Author(s): Martinez-Carranza, M., Sauguet, L.
• Funding Organization(s): Agence Nationale de la Recherche (ANR), H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.91 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 39738083 
• DOI: https://doi.org/10.1038/s41467-024-55365-w
• Primary Citation 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.

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Organizational Affiliation: 
• Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.
Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), Plouzané, France.
Biological NMR & HDX-MS Technological Platform, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.
Structural Bioinformatics, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.
Department of Molecular Biology and Genetics, Van Yüzüncü Yil University, Van, Turkey.
Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.
Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, Saint-Aubin, France.
Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.
Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), Plouzané, France. [e-mail].
Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 233.95 kDa 
• Atom Count: 13,557 
• Modeled Residue Count: 1,692 
• Deposited Residue Count: 2,064 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase II small subunit	A	662	Pyrococcus abyssi GE5	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase II large subunit	B	1,270	Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: polC, PF0019 EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (PDB Primary Data)
UniProt
Find proteins for Q9V2F4 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2F4  Go to UniProtKB:  Q9V2F4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination	C	132	Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: PAB2165
UniProt
Find proteins for Q9V1Z1 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V1Z1  Go to UniProtKB:  Q9V1Z1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth B], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.91 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.4

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Martinez-Carranza, M., Sauguet, L.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--
H2020 Marie Curie Actions of the European Commission	European Union	--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Data collection, Database references
• Version 1.2: 2025-07-02
  Changes: Data collection