4KOP

Crystal Structure of WHY2 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A family portrait: structural comparison of the Whirly proteins from Arabidopsis thaliana and Solanum tuberosum.

Cappadocia, L.Parent, J.S.Sygusch, J.Brisson, N.

(2013) Acta Crystallogr.,Sect.F 69: 1207-1211

  • DOI: 10.1107/S1744309113028698
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA double-strand breaks are highly detrimental genomic lesions that routinely arise in genomes. To protect the integrity of their genetic information, all organisms have evolved specialized DNA-repair mechanisms. Whirly proteins modulate DNA repair ...

    DNA double-strand breaks are highly detrimental genomic lesions that routinely arise in genomes. To protect the integrity of their genetic information, all organisms have evolved specialized DNA-repair mechanisms. Whirly proteins modulate DNA repair in plant chloroplasts and mitochondria by binding single-stranded DNA in a non-sequence-specific manner. Although most of the results showing the involvement of the Whirly proteins in DNA repair have been obtained in Arabidopsis thaliana, only the crystal structures of the potato Whirly proteins WHY1 and WHY2 have been reported to date. The present report of the crystal structures of the three Whirly proteins from A. thaliana (WHY1, WHY2 and WHY3) reveals that these structurally similar proteins assemble into tetramers. Furthermore, structural alignment with a potato WHY2-DNA complex reveals that the residues in these proteins are properly oriented to bind single-stranded DNA in a non-sequence-specific manner.


    Organizational Affiliation

    Department of Biochemistry, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, Québec H3C 3J7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Single-stranded DNA-binding protein WHY2, mitochondrial
A, B, C, D
177Arabidopsis thalianaMutation(s): 0 
Gene Names: WHY2
Find proteins for Q8VYF7 (Arabidopsis thaliana)
Go to UniProtKB:  Q8VYF7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPO
Query on MPO

Download SDF File 
Download CCD File 
A, B, C, D
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.470α = 90.00
b = 72.661β = 90.00
c = 136.834γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data collection
SCALEPACKdata scaling
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description