8AAJ

Crystal structure of the Pyrococcus abyssi RPA (apo form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

DNA-binding mechanism and evolution of replication protein A.

Madru, C.Martinez-Carranza, M.Laurent, S.Alberti, A.C.Chevreuil, M.Raynal, B.Haouz, A.Le Meur, R.A.Delarue, M.Henneke, G.Flament, D.Krupovic, M.Legrand, P.Sauguet, L.

(2023) Nat Commun 14: 2326-2326

  • DOI: https://doi.org/10.1038/s41467-023-38048-w
  • Primary Citation of Related Structures:  
    8AA9, 8AAJ, 8AAS, 8C5Y, 8C5Z, 8OEJ, 8OEL

  • PubMed Abstract: 

    Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in 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
Replication factor A358Pyrococcus abyssi GE5Mutation(s): 1 
Gene Names: PAB2163
UniProt
Find proteins for Q9V1Y9 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V1Y9 
Go to UniProtKB:  Q9V1Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V1Y9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination268Pyrococcus abyssi GE5Mutation(s): 1 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RPA14 subunit of the hetero-oligomeric complex involved in homologous recombination122Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: PAB2164
UniProt
Find proteins for Q9V1Z0 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V1Z0 
Go to UniProtKB:  Q9V1Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V1Z0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.526α = 90
b = 169.738β = 90
c = 201.855γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
SHELXDphasing
PHASERphasing
PARROTphasing
MxCuBEdata collection
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-JCJC-1501 ARCHPOL
Agence Nationale de la Recherche (ANR)FranceANR-20-CE11-0003 ARCHAPRIM

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release