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

Experimental Data Snapshot

  • Resolution: 1.38 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/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 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.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cold shock protein cspB
A, B
67Bacillus subtilisMutation(s): 0 
Gene Names: BSU09100cspAcspB
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: 2
MoleculeChains LengthOrganismImage
hexaribonucleotide (rGUCUUUA)C [auth R]7N/A
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description