3PF4

Crystal structure of Bs-CspB in complex with r(GUCUUUA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution.

Sachs, R.Max, K.E.Heinemann, U.Balbach, J.

(2012) RNA 18: 65-76

  • DOI: 10.1261/rna.02809212
  • Primary Citation of Related Structures:  
    3PF4, 3PF5

  • PubMed Abstract: 
  • Bacterial cold shock proteins (CSPs) regulate the cellular response to temperature downshift. Their general principle of function involves RNA chaperoning and transcriptional antitermination. Here we present two crystal structures of cold shock prote ...

    Bacterial cold shock proteins (CSPs) regulate the cellular response to temperature downshift. Their general principle of function involves RNA chaperoning and transcriptional antitermination. Here we present two crystal structures of cold shock protein B from Bacillus subtilis (Bs-CspB) in complex with either a hexanucleotide (5'-UUUUUU-3') or heptanucleotide (5'-GUCUUUA-3') single-stranded RNA (ssRNA). Hydrogen bonds and stacking interactions between RNA bases and aromatic sidechains characterize individual binding subsites. Additional binding subsites which are not occupied by the ligand in the crystal structure were revealed by NMR spectroscopy in solution on Bs-CspB·RNA complexes. Binding studies demonstrate that Bs-CspB associates with ssDNA as well as ssRNA with moderate sequence specificity. Varying affinities of oligonucleotides are reflected mainly in changes of the dissociation rates. The generally lower binding affinity of ssRNA compared to its ssDNA analog is attributed solely to the substitution of thymine by uracil bases in RNA.


    Organizational Affiliation

    Fachgruppe Biophysik Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cold shock protein cspBAB67Bacillus subtilisMutation(s): 0 
Gene Names: BSU09100cspAcspB
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: 2
    MoleculeChainsLengthOrganismImage
    hexaribonucleotide (rGUCUUUA)R7N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download CCD File 
    A
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download CCD File 
    A
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.38 Å
    • R-Value Free: 0.194 
    • R-Value Work: 0.154 
    • R-Value Observed: 0.156 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 49.275α = 90
    b = 50.512β = 90
    c = 57.802γ = 90
    Software Package:
    Software NamePurpose
    XSCALEdata scaling
    PHASERphasing
    REFMACrefinement
    PDB_EXTRACTdata extraction
    HKL-2000data collection
    XDSdata reduction

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2011-09-21
      Type: Initial release
    • Version 1.1: 2011-12-14
      Changes: Database references
    • Version 1.2: 2011-12-28
      Changes: Database references