BMRB Entry 17225

Name: The Solution Structure and DNA-binding Properties of the Cold-shock Domain of the Human Y-box Protein YB-1
Published: 2010-11-10

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17225

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2010-09-29

Original release date:

2010-11-10

Authors:

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

Citation:

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).
PubMed: 11851341

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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

Data sets:

binding_constants

Data type	Count
binding constants	2

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CSD	1
2	ssDNA	2

Entities:

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

1

MET

LYS

VAL

ILE

ALA

THR

LYS

VAL

LEU

2

GLY

THR

VAL

LYS

TRP

PHE

ASN

VAL

ARG

ASN

3

GLY

TYR

GLY

PHE

ILE

ASN

ARG

ASN

ASP

THR

4

LYS

GLU

ASP

VAL

PHE

VAL

HIS

GLN

THR

ALA

5

ILE

LYS

ASN

PRO

ARG

LYS

TYR

LEU

6

ARG

SER

VAL

GLY

ASP

GLY

GLU

THR

VAL

GLU

7

PHE

ASP

VAL

GLU

GLY

GLU

LYS

GLY

ALA

8

GLU

ALA

ASN

VAL

THR

GLY

PRO

GLY

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

1

DA

DT

DG

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_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

BMRB	4147
PDB	1H95
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
AlphaFold	P16989 P21573 P62960 P62961 P67808