9F2A image
Deposition Date 2024-04-22
Release Date 2024-12-04
Last Version Date 2025-07-02
Entry Detail
PDB ID:
9F2A
Keywords:
Title:
Pyrococcus abyssi PolD in complex with Rpa2 winged-helix domain class 2 (composite map)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.91 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase II small subunit
Gene (Uniprot):polB
Chain IDs:A
Chain Length:662
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA polymerase II large subunit
Gene (Uniprot):polC
Chain IDs:B
Chain Length:1270
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination
Gene (Uniprot):PAB2165
Chain IDs:C
Chain Length:132
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Primary Citation
Communication between DNA polymerases and Replication Protein A within the archaeal replisome.
Nat Commun 15 10926 10926 (2024)
PMID: 39738083 DOI: 10.1038/s41467-024-55365-w

Abstact

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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Primary Citation of related structures
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