BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 17225

Title: The Solution Structure and DNA-binding Properties of the Cold-shock Domain of the Human Y-box Protein YB-1   PubMed: 11851341

Authors: Kloks, Cathelijne; Spronk, Christian; Lasonder, Edwin; Hoffmann, Astrid; Vuister, Geerten; Grzesiek, Stephan; Hilbers, Cornelis

Citation: Kloks, Cathelijne; Spronk, Christian; Lasonder, Edwin; Hoffmann, Astrid; Vuister, Geerten; Grzesiek, Stephan; Hilbers, Cornelis. "The Solution Structure and DNA-binding Properties of the Cold-shock Domain of the Human Y-box Protein YB-1"  J. Mol. Biol. 316, 317-326 (2002).

Assembly members:
CSD, polymer, 79 residues, Formula weight is not available
ssDNA, polymer, 5 residues, Formula weight is not available

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
CSD: MKKVIATKVLGTVKWFNVRN GYGFINRNDTKEDVFVHQTA IKKNNPRKYLRSVGDGETVE FDVVEGEKGAEAANVTGPG
ssDNA: ATTGG

Data sets:
  • assigned_chemical_shifts
  • binding_constants
Data typeCount
binding constants2

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1CSD1
2ssDNA2

Entities:

Entity 1, CSD 79 residues - Formula weight is not available

1   METLYSLYSVALILEALATHRLYSVALLEU
2   GLYTHRVALLYSTRPPHEASNVALARGASN
3   GLYTYRGLYPHEILEASNARGASNASPTHR
4   LYSGLUASPVALPHEVALHISGLNTHRALA
5   ILELYSLYSASNASNPROARGLYSTYRLEU
6   ARGSERVALGLYASPGLYGLUTHRVALGLU
7   PHEASPVALVALGLUGLYGLULYSGLYALA
8   GLUALAALAASNVALTHRGLYPROGLY

Entity 2, ssDNA 5 residues - Formula weight is not available

1   DADTDTDGDG

Samples:

sample_1: CSD 2.7 mg; ssDNA0 – 2 equivalents; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.7; pressure: ambient atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PIPP, Garrett, D. S., Powers, R., Gronenborn, A. M. & Clore, G. M. - peak picking

NMR spectrometers:

  • Bruker DRX 500 MHz
  • Varian UnityInova 750 MHz

Related Database Links:

BMRB 4147
PDB
DBJ BAA02569 BAA03376 BAA05380 BAA19849 BAC45236
EMBL CAA40847 CAA42778 CAA51261 CAA64631 CAB46826
GB AAA02573 AAA20871 AAA21677 AAA30497 AAA35749
PRF 2210343A
REF NP_001003127 NP_001016677 NP_001076254 NP_001079367 NP_001080330
SP P16989 P21573 P62960 P62961 P67808
TPG DAA29365 DAA30957