4NOE

Crystal structure of DdrB bound to 30b ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism for accurate, protein-assisted DNA annealing by Deinococcus radiodurans DdrB.

Sugiman-Marangos, S.N.Weiss, Y.M.Junop, M.S.

(2016) Proc.Natl.Acad.Sci.USA 113: 4308-4313

  • DOI: 10.1073/pnas.1520847113

  • PubMed Abstract: 
  • Accurate pairing of DNA strands is essential for repair of DNA double-strand breaks (DSBs). How cells achieve accurate annealing when large regions of single-strand DNA are unpaired has remained unclear despite many efforts focused on understanding p ...

    Accurate pairing of DNA strands is essential for repair of DNA double-strand breaks (DSBs). How cells achieve accurate annealing when large regions of single-strand DNA are unpaired has remained unclear despite many efforts focused on understanding proteins, which mediate this process. Here we report the crystal structure of a single-strand annealing protein [DdrB (DNA damage response B)] in complex with a partially annealed DNA intermediate to 2.2 Å. This structure and supporting biochemical data reveal a mechanism for accurate annealing involving DdrB-mediated proofreading of strand complementarity. DdrB promotes high-fidelity annealing by constraining specific bases from unauthorized association and only releases annealed duplex when bound strands are fully complementary. To our knowledge, this mechanism provides the first understanding for how cells achieve accurate, protein-assisted strand annealing under biological conditions that would otherwise favor misannealing.


    Organizational Affiliation

    Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8N 3Z5, Canada;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Single-stranded DNA-binding protein DdrB
A, B, C, D, E
148Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Mutation(s): 0 
Gene Names: ddrB
Find proteins for Q9RY80 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RY80
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP*TP*TP*GP*CP*GP*CP)-3'F30N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 131.760α = 90.00
b = 131.760β = 90.00
c = 102.280γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
CBASSdata collection
MOSFLMdata reduction
PHENIXmodel building
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references
  • Version 1.2: 2016-04-20
    Type: Database references
  • Version 1.3: 2016-05-04
    Type: Database references