4GOP

Structure and Conformational Change of a Replication Protein A Heterotrimer Bound to ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

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This is version 1.1 of the entry. See complete history


Literature

Structure and conformational change of a replication protein A heterotrimer bound to ssDNA.

Fan, J.Pavletich, N.P.

(2012) Genes Dev 26: 2337-2347

  • DOI: https://doi.org/10.1101/gad.194787.112
  • Primary Citation of Related Structures:  
    4GOP

  • PubMed Abstract: 

    Replication protein A (RPA) is the main eukaryotic ssDNA-binding protein with essential roles in DNA replication, recombination, and repair. RPA maintains the DNA as single-stranded and also interacts with other DNA-processing proteins, coordinating their assembly and disassembly on DNA. RPA binds to ssDNA in two conformational states with opposing affinities for DNA and proteins. The RPA-protein interactions are compatible with a low DNA affinity state that involves DNA-binding domain A (DBD-A) and DBD-B but not with the high DNA affinity state that additionally engages DBD-C and DBD-D. The structure of the high-affinity RPA-ssDNA complex reported here shows a compact quaternary structure held together by a four-way interface between DBD-B, DBD-C, the intervening linker (BC linker), and ssDNA. The BC linker binds into the DNA-binding groove of DBD-B, mimicking DNA. The associated conformational change and partial occlusion of the DBD-A-DBA-B protein-protein interaction site establish a mechanism for the allosteric coupling of RPA-DNA and RPA-protein interactions.


  • Organizational Affiliation

    Sloan-Kettering Division, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinA,
D [auth X]
114Mycosarcoma maydisMutation(s): 0 
Gene Names: UM04165.1
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinB,
E [auth Y]
136Mycosarcoma maydisMutation(s): 0 
Gene Names: UM02579.1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinC,
F [auth Z]
444Mycosarcoma maydisMutation(s): 0 
Gene Names: UM05156.1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (25-MER)G [auth K],
H [auth L]
32synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.1α = 90
b = 93.8β = 110.9
c = 120.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary