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Structure of the human Replication Protein A (RPA) trimerization core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA.

Bochkareva, E.Korolev, S.Lees-Miller, S.P.Bochkarev, A.

(2002) EMBO J 21: 1855-1863

  • DOI: 10.1093/emboj/21.7.1855
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The human single-stranded DNA-binding protein, replication protein A (RPA) binds DNA in at least two different modes: initial [8-10 nucleotides (nt)] and stable ( approximately 30 nt). Switching from 8 to 30 nt mode is associated with a large conform ...

    The human single-stranded DNA-binding protein, replication protein A (RPA) binds DNA in at least two different modes: initial [8-10 nucleotides (nt)] and stable ( approximately 30 nt). Switching from 8 to 30 nt mode is associated with a large conformational change. Here we report the 2.8 A structure of the RPA trimerization core comprising the C-terminal DNA-binding domain of subunit RPA70 (DBD-C), the central DNA-binding domain of subunit RPA32 (DBD-D) and the entire RPA14 subunit. All three domains are built around a central oligonucleotide/oligosaccharide binding (OB)-fold and flanked by a helix at the C-terminus. Trimerization is mediated by three C-terminal helices arranged in parallel. The OB-fold of DBD-C possesses unique structural features; embedded zinc ribbon and helix-turn-helix motifs. Using time-resolved proteolysis with trypsin, we demonstrate that the trimerization core does not contribute to the binding with substrates of 10 nt, but interacts with oligonucleotides of 24 nt. Taken together, our data indicate that switching from 8-10 to 30 nt mode is mediated by DNA binding with the trimerization core.


    Related Citations: 
    • The role for zinc in replication protein A.
      Bochkareva, E., Korolev, S., Bochkarev, A.
      (2000) J Biol Chem 275: 27332

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73190, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replication protein A 14 kDa subunit
A, D
121Homo sapiensMutation(s): 0 
Gene Names: RFA3_HUMANRPA3REPA3RPA14
Find proteins for P35244 (Homo sapiens)
Go to UniProtKB:  P35244
NIH Common Fund Data Resources
PHAROS  P35244

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Replication protein A 32 kDa subunit
B, E
128Homo sapiensMutation(s): 0 
Gene Names: RFA2_HUMANRPA2REPA2RPA32RPA34
Find proteins for P15927 (Homo sapiens)
Go to UniProtKB:  P15927
NIH Common Fund Data Resources
PHAROS  P15927

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Replication protein A 70 kDa DNA-binding subunit
C, F
181Homo sapiensMutation(s): 0 
Gene Names: RFA1_HUMANRPA1REPA1RPA70
Find proteins for P27694 (Homo sapiens)
Go to UniProtKB:  P27694
NIH Common Fund Data Resources
PHAROS  P27694
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
C, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.527α = 90
b = 88.527β = 90
c = 341.09γ = 120
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-05
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance