2GDJ

Delta-62 RADA recombinase in complex with AMP-PNP and magnesium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Rad51/RadA N-Terminal Domain Activates Nucleoprotein Filament ATPase Activity.

Galkin, V.E.Wu, Y.Zhang, X.-P.Qian, X.He, Y.Yu, X.Heyer, W.-D.Luo, Y.Egelman, E.H.

(2006) Structure 14: 983-992

  • DOI: 10.1016/j.str.2006.04.001
  • Primary Citation of Related Structures:  
    2GDJ

  • PubMed Abstract: 
  • Proteins in the RecA/RadA/Rad51 family form helical filaments on DNA that function in homologous recombination. While these proteins all have the same highly conserved ATP binding core, the RadA/Rad51 proteins have an N-terminal domain that shows no homology with the C-terminal domain found in RecA ...

    Proteins in the RecA/RadA/Rad51 family form helical filaments on DNA that function in homologous recombination. While these proteins all have the same highly conserved ATP binding core, the RadA/Rad51 proteins have an N-terminal domain that shows no homology with the C-terminal domain found in RecA. Both the Rad51 N-terminal and RecA C-terminal domains have been shown to bind DNA, but no role for these domains has been established. We show that RadA filaments can be trapped in either an inactive or active conformation with respect to the ATPase and that activation involves a large rotation of the subunit aided by the N-terminal domain. The G103E mutation within the yeast Rad51 N-terminal domain inactivates the filament by failing to make proper contacts between the N-terminal domain and the core. These results show that the N-terminal domains play a regulatory role in filament activation and highlight the modular architecture of the recombination proteins.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Virginia, Box 800733, Charlottesville, Virginia 22908, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair and recombination protein radAA264Methanococcus voltaeMutation(s): 0 
Gene Names: radA
UniProt
Find proteins for O73948 (Methanococcus voltae)
Explore O73948 
Go to UniProtKB:  O73948
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.75α = 90
b = 67.75β = 90
c = 90.08γ = 120
Software Package:
Software NamePurpose
SAINTPLUSdata collection
LSCALEdata reduction
AMoREphasing
CNSrefinement
SAINTdata reduction
LSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description