3N1J

Crystal structure of a StWhy2-dT32 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair.

Cappadocia, L.Marechal, A.Parent, J.S.Lepage, E.Sygusch, J.Brisson, N.

(2010) Plant Cell 22: 1849-1867

  • DOI: 10.1105/tpc.109.071399
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanism ...

    DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanisms of DNA repair in these organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant organelle genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.


    Organizational Affiliation

    Department of Biochemistry, Université de Montréal, Montreal, Canada H3C 3J7.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein StWhy2
A
178Solanum tuberosumMutation(s): 0 
Gene Names: WHY2
Find proteins for D9J034 (Solanum tuberosum)
Go to UniProtKB:  D9J034
Entity ID: 2
MoleculeChainsLengthOrganism
DNA 32-mer dT32B9N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.211 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 166.495α = 90.00
b = 166.495β = 90.00
c = 166.495γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CNSphasing
PHENIXrefinement
PHENIXmodel building
CNSrefinement
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2019-07-17
    Type: Data collection, Refinement description