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

Experimental Data Snapshot

  • Resolution: 1.78 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.jmb.2006.05.044
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

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


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cold shock protein cspBB [auth A]67Bacillus subtilisMutation(s): 0 
Gene Names: cspBcspA
Find proteins for P32081 (Bacillus subtilis (strain 168))
Explore P32081 
Go to UniProtKB:  P32081
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32081
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*TP*TP*TP*TP*TP*T)-3'A [auth B]6N/A
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.78 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.03α = 90
b = 53.17β = 90
c = 76.94γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description