Macromolecule Content

• Total Structure Weight: 8.75 kDa 
• Atom Count: 617 
• Modelled Residue Count: 79 
• Deposited Residue Count: 79 
• Unique protein chains: 1

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)

• DOI: 10.2210/pdb1H95/pdb
• BMRB: 4147

• Classification: TRANSLATION FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-02-23 Released: 2002-02-21 
• Deposition Author(s): Kloks, C.P.A.M., Spronk, C.A.E.M., Hoffmann, A., Vuister, G.W., Grzesiek, S., Hilbers, C.W.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 

Literature

The Solution Structure and DNA-Binding Properties of the Cold-Shock Domain of the Human Y-Box Protein Yb-1.

Kloks, C.P.A.M., Spronk, C.A.E.M., Lasonder, E., Hoffmann, A., Vuister, G.W., Grzesiek, S., Hilbers, C.W.

(2002) J Mol Biol 316: 317

• PubMed: 11851341 
• DOI: 10.1006/jmbi.2001.5334
• Primary Citation of Related Structures:  
  1H95


• 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.

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Organizational Affiliation: 

NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Y-BOX BINDING PROTEIN	A	79	Homo sapiens	Mutation(s): 0  Gene Names: YBX1, NSEP1, YB1
Find proteins for P67809 (Homo sapiens) Explore P67809  Go to UniProtKB:  P67809
NIH Common Fund Data Resources
PHAROS:  P67809 GTEx:  ENSG00000065978

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• OLDERADO: 1H95 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-02-23 
• Released Date: 2002-02-21 
Deposition Author(s): Kloks, C.P.A.M., Spronk, C.A.E.M., Hoffmann, A., Vuister, G.W., Grzesiek, S., Hilbers, C.W.

Revision History  

• Version 1.0: 2002-02-21
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance