3PF4

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

Summary for 3PF4

• Entry DOI: 10.2210/pdb3pf4/pdb
• Related: 1C9O 1CSP 2ES2 2F52 2HAX
• Descriptor: Cold shock protein cspB, hexaribonucleotide (rGUCUUUA), SODIUM ION, ... (5 entities in total)
• Functional Keywords: beta barrel, protein-rna complex, cold shock response, transcription regulation, translation regulation, ob fold, cold shock domain, rna/dna binding, single-stranded rna and dna, cytosol, gene regulation-rna complex, gene regulation/rna
• Biological source: Bacillus subtilis; More
• Cellular location: Cytoplasm: P32081
• Total number of polymer chains: 3
• Total formula weight: 16950.85

Authors

Sachs, R.,Max, K.E.A.,Heinemann, U. (deposition date: 2010-10-27, release date: 2011-09-21, Last modification date: 2023-09-06)

Primary citation

Sachs, R.,Max, K.E.,Heinemann, U.,Balbach, J.
RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution.
Rna, 18:65-76, 2012

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.

PubMed: 22128343
DOI: 10.1261/rna.02809212

Experimental method

X-RAY DIFFRACTION (1.38 Å)