9F29

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

• PDB DOI: https://doi.org/10.2210/pdb9F29/pdb
• EM Map EMD-50140: 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), Fondation pour la Recherche Medicale (FRM), H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

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

Literature

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

Martinez-Carranza, M., Sauguet, L.

To be published.

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: 13,520 
• Modelled Residue Count: 1,688 
• Deposited Residue Count: 2,064 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination	A [auth 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase II small subunit	B [auth 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase II large subunit	C [auth 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 P81409 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P81409  Go to UniProtKB:  P81409

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: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
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	--
Fondation pour la Recherche Medicale (FRM)	France	--
H2020 Marie Curie Actions of the European Commission	European Union	--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release