1H95

Solution structure of the single-stranded DNA-binding Cold Shock Domain (CSD) of human Y-box protein 1 (YB1) determined by NMR (10 lowest energy structures)

Summary for 1H95

• Entry DOI: 10.2210/pdb1h95/pdb
• NMR Information: BMRB: 4147
• Descriptor: Y-BOX BINDING PROTEIN (1 entity in total)
• Functional Keywords: translation factor, transcription factor, ob-fold, 5-stranded anti-parallel beta-barrel, single stranded dna binding, cold shock, y-box
• Biological source: HOMO SAPIENS (HUMAN)
• Total number of polymer chains: 1
• Total formula weight: 8754.90

Authors

Kloks, C.P.A.M.,Spronk, C.A.E.M.,Hoffmann, A.,Vuister, G.W.,Grzesiek, S.,Hilbers, C.W. (deposition date: 2001-02-23, release date: 2002-02-21, Last modification date: 2024-05-15)

Primary citation

Kloks, C.P.A.M.,Spronk, C.A.E.M.,Lasonder, E.,Hoffmann, A.,Vuister, G.W.,Grzesiek, S.,Hilbers, C.W.
The Solution Structure and DNA-Binding Properties of the Cold-Shock Domain of the Human Y-Box Protein Yb-1.
J.Mol.Biol., 316:317-, 2002

PubMed Abstract: The human Y-box protein 1 (YB-1) is a member of the Y-box protein family, a class of proteins involved in transcriptional and translational regulation of a wide range of genes. Here, we report the solution structure of the cold-shock domain (CSD) of YB-1, which is thought to be responsible for nucleic acid binding. It is the first structure solved of a eukaryotic member of the cold-shock protein family and consists of a closed five-stranded anti-parallel beta-barrel capped by a long flexible loop. The structure of CSD is similar to the OB-fold and a comparison with bacterial cold-shock proteins shows that its structural properties are conserved from bacteria to man. Our data suggest the presence of a DNA-binding site consisting of a patch of positively charged and aromatic residues on the surface of the beta-barrel. Further, it is shown that CSD, which has a preference for binding single-stranded pyrimidine-rich sequences, binds weakly and hardly specifically to DNA. Binding affinities reported for intact YB-1 indicate that domains other than the CSD play a role in DNA binding of YB-1.

PubMed: 11851341
DOI: 10.1006/JMBI.2001.5334

Experimental method

SOLUTION NMR