2ES2

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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This is version 1.2 of the entry. See complete history. 


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

  • DOI: 10.1016/j.jmb.2006.05.044
  • Primary Citation of Related Structures:  
    2ES2

  • 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 ...

    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.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cold shock protein cspBA67Bacillus subtilisMutation(s): 0 
Gene Names: cspB, cspA
Find proteins for P32081 (Bacillus subtilis (strain 168))
Explore P32081 
Go to UniProtKB:  P32081
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*TP*TP*TP*TP*T)-3'B6N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CA
    Query on CA
    Download Ideal Coordinates CCD File 
    A
    		CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • 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
    AMoREphasing
    REFMACrefinement
    PDB_EXTRACTdata extraction
    XDSdata reduction

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History 

    • 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