Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78.91 kDa 
• Atom Count: 2017 
• Residue Count: 222 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3VDY

B. subtilis SsbB/ssDNA

• DOI: 10.2210/pdb3VDY/pdb
• NDB: NA1593

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Bacillus subtilis, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-06 Released: 2012-03-14 
• Deposition Author(s): Yadav, T., Carrasco, B., Myers, A.R., George, N.P., Keck, J.L., Alonso, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Genetic recombination in Bacillus subtilis: a division of labor between two single-strand DNA-binding proteins.

Yadav, T., Carrasco, B., Myers, A.R., George, N.P., Keck, J.L., Alonso, J.C.

(2012) Nucleic Acids Res 40: 5546-5559

• PubMed: 22373918 
• DOI: 10.1093/nar/gks173
• Primary Citation of Related Structures:  
  3VDY


• PubMed Abstract: 
  

We have investigated the structural, biochemical and cellular roles of the two single-stranded (ss) DNA-binding proteins from Bacillus subtilis, SsbA and SsbB. During transformation, SsbB localizes at the DNA entry pole where it binds and protects internalized ssDNA. The 2.8-Å resolution structure of SsbB bound to ssDNA reveals a similar overall protein architecture and ssDNA-binding surface to that of Escherichia coli SSB. SsbA, which binds ssDNA with higher affinity than SsbB, co-assembles onto SsbB-coated ssDNA and the two proteins inhibit ssDNA binding by the recombinase RecA. During chromosomal transformation, the RecA mediators RecO and DprA provide RecA access to ssDNA. Interestingly, RecO interaction with ssDNA-bound SsbA helps to dislodge both SsbA and SsbB from the DNA more efficiently than if the DNA is coated only with SsbA. Once RecA is nucleated onto the ssDNA, RecA filament elongation displaces SsbA and SsbB and enables RecA-mediated DNA strand exchange. During plasmid transformation, RecO localizes to the entry pole and catalyzes annealing of SsbA- or SsbA/SsbB-coated complementary ssDNAs to form duplex DNA with ssDNA tails. Our results provide a mechanistic framework for rationalizing the coordinated events modulated by SsbA, SsbB and RecO that are crucial for RecA-dependent chromosomal transformation and RecA-independent plasmid transformation.

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Organizational Affiliation: 

Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein ssbB	A, B	116	Bacillus subtilis	Mutation(s): 0  Gene Names: ssbB, ywpH, BSU36310
Find proteins for C0SPB6 (Bacillus subtilis (strain 168)) Explore C0SPB6  Go to UniProtKB:  C0SPB6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'	C, D, E, F, G	35	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.753	α = 90
b = 101.753	β = 90
c = 118.571	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-06 
• Released Date: 2012-03-14 
Deposition Author(s): Yadav, T., Carrasco, B., Myers, A.R., George, N.P., Keck, J.L., Alonso, J.C.

Revision History 

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Database references