9F28 | pdb_00009f28

Crystal structure of the heterodimeric primase from pyrococcus abyssi (deletion of the PriL-CTD domain)

• PDB DOI: https://doi.org/10.2210/pdb9F28/pdb

• Classification: REPLICATION
• Organism(s): Pyrococcus abyssi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-22 Released: 2024-12-04 
• Deposition Author(s): Madru, C., Sauguet, L.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.224 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

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.

---

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 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.4 kDa 
• Atom Count: 5,234 
• Modeled Residue Count: 555 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase small subunit PriS	A	351	Pyrococcus abyssi	Mutation(s): 0  Gene Names: priS, priA, PYRAB01820, PAB2236 EC: 2.7.7
UniProt
Find proteins for Q9V292 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V292  Go to UniProtKB:  Q9V292

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase large subunit PriL	B	223	Pyrococcus abyssi	Mutation(s): 0  Gene Names: priL, priB, PYRAB01830, PAB2235
UniProt
Find proteins for Q9V291 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V291  Go to UniProtKB:  Q9V291

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	F [auth A], G [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.224 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.574	α = 90
b = 116.574	β = 90
c = 121.084	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Madru, C., Sauguet, L.

---

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ARCHAPOL

Revision History  

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