8AAS

Crystal structure of the Pyrococcus abyssi RPA trimerization core bound to poly-dT20 ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.266 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.1 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 A295Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: PAB2163
UniProt
Find proteins for G8ZHS0 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore G8ZHS0 
Go to UniProtKB:  G8ZHS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8ZHS0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination183Pyrococcus abyssi GE5Mutation(s): 0 
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
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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

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')D [auth F]20synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.266 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.234α = 90
b = 75.234β = 90
c = 215.487γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
MxCuBEdata collection
Cootmodel building

Structure Validation

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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
  • Version 1.1: 2024-05-01
    Changes: Data collection, Refinement description