2HAX

Crystal structure of Bacillus caldolyticus cold shock protein in complex with hexathymidine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus.

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

(2007) FEBS J 274: 1265-1279

  • DOI: 10.1111/j.1742-4658.2007.05672.x
  • Primary Citation of Related Structures:  
    2HAX

  • PubMed Abstract: 

    • Bacterial cold shock proteins (CSPs) regulate cellular adaptation to cold stress. Functions ascribed to CSP include roles as RNA chaperones and in transcription antitermination. We present the crystal structure of the Bacillus caldolyticus CSP (Bc-Csp) in complex with hexathymidine (dT(6)) at a resolution of 1 ...

    Bacterial cold shock proteins (CSPs) regulate cellular adaptation to cold stress. Functions ascribed to CSP include roles as RNA chaperones and in transcription antitermination. We present the crystal structure of the Bacillus caldolyticus CSP (Bc-Csp) in complex with hexathymidine (dT(6)) at a resolution of 1.29 A. Bound to dT(6), crystalline Bc-Csp forms a domain-swapped dimer in which beta strands 1-3 associate with strands 4 and 5 from the other subunit to form a closed beta barrel and vice versa. The globular units of dimeric Bc-Csp closely resemble the well-known structure of monomeric CSP. Structural reorganization from the monomer to the domain-swapped dimer involves a strictly localized change in the peptide bond linking Glu36 and Gly37 of Bc-Csp. Similar structural reorganizations have not been found in any other CSP or oligonucleotide/oligosaccharide-binding fold structures. Each dT(6) ligand is bound to one globular unit of Bc-Csp via an amphipathic protein surface. Individual binding subsites interact with the DNA bases through stacking and hydrogen bonding. The sugar-phosphate backbone remains solvent exposed. Based on crystallographic and biochemical studies of deoxyoligonucleotide binding to CSP, we suggest a common mode of binding of single-stranded heptanucleotide motifs to proteins containing cold shock domains, including the eukaryotic Y-box factors.

    Organizational Affiliation: 

    Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin-Buch, Germany.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cold shock protein cspBC [auth A],
D [auth B]		66[Bacillus] caldolyticusMutation(s): 0 
Gene Names: cspB
UniProt
Find proteins for P41016 (Bacillus caldolyticus)
Explore P41016 
Go to UniProtKB:  P41016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41016
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*TP*TP*TP*TP*T)-3'A [auth C],
B [auth D]		6N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD
Download Ideal Coordinates CCD File 
F [auth A],
G [auth B]		(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.34α = 90
b = 64.89β = 90
c = 31.2γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description