Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9232.48 
• Atom Count: 631 
• Residue Count: 73 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2ES2

Crystal Structure Analysis of the Bacillus Subtilis Cold Shock Protein Bs-CspB in Complex with Hexathymidine

• DOI: 10.2210/pdb2ES2/pdb
• NDB: PD0726

• Classification: GENE REGULATION
• Organism(s): Bacillus subtilis (strain 168)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2005-10-25 Released: 2006-09-05 
• Deposition Author(s): Max, K.E.A., Bienert, M., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.223 
• R-Value Work: 0.189 

Literature

T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB.

Max, K.E., Zeeb, M., Bienert, R., Balbach, J., Heinemann, U.

(2006) J.Mol.Biol. 360: 702-714

• PubMed: 16780871 
• DOI: 10.1016/j.jmb.2006.05.044


• PubMed Abstract: 
  

Bacterial cold shock proteins (CSPs) are involved in cellular adaptation to cold stress. They bind to single-stranded nucleic acids with a KD value in the micro- to nanomolar range. Here we present the structure of the Bacillus subtilis CspB (Bs-CspB) in complex with hexathymidine (dT6) at a resolution of 1.78 A. Bs-CspB binds to dT6 with nanomolar affinity via an amphipathic interface on the protein surface. Individual binding subsites interact with single nucleobases through stacking interactions and hydrogen bonding. The sugar-phosphate backbone and the methyl groups of the thymine nucleobases remain solvent exposed and are not contacted by protein groups. Fluorescence titration experiments monitoring the binding of oligopyrimidines to Bs-CspB reveal binding preferences at individual subsites and allow the design of an optimised heptapyrimidine ligand, which is bound with sub-nanomolar affinity. This study reveals the stoichiometry and sequence determinants of the binding of single-stranded nucleic acids to a preformed site on Bs-CspB and thus provides the structural basis of the RNA chaperone and transcription antitermination activities of the CSP.

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Organizational Affiliation: 

Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Cold shock protein cspB	A	67	Bacillus subtilis (strain 168)	Mutation(s): 0  Gene Names: cspB (cspA)
Find proteins for P32081 (Bacillus subtilis (strain 168)) Go to UniProtKB:  P32081

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*TP*TP*TP*TP*TP*T)-3'	B	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.223 
• R-Value Work: 0.189 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 49.030	α = 90.00
b = 53.170	β = 90.00
c = 76.940	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
AMoRE	phasing
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-25 
• Released Date: 2006-09-05 
• Deposition Author(s): Max, K.E.A., Bienert, M., Heinemann, U.

Revision History 

• Version 1.0: 2006-09-05
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance