Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR53597

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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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Name: 1H-15N backbone assignment of the ssDNA-bound form of YB-1 refolded Cold Shock Domain.
Published: 2026-03-09

Title:

1H-15N backbone assignment of the ssDNA-bound form of YB-1 refolded Cold Shock Domain.

Deposition date:

2026-03-03

Original release date:

2026-03-09

Authors:

Grasso, Daniela; Gedi, Vinayakumar; Bernini, Andrea; Prischi, Filippo

Citation:

Citation: Grasso, Daniela; Gedi, Vinayakumar; Bernini, Andrea; Prischi, Filippo. "DNA Binding to the Cold Shock Domain of YB1 Enables its Phosphorylation by RSK4" .

Assembly members:

Assembly members:
entity_1, polymer, 93 residues, Formula weight is not available
entity_2, polymer, 7 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: pETM14

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPMDKKVIATKVLGTVKWFN VRNGYGFINRNDTKEDVFVH QTAIKKNNPRKYLRSVGDGE TVEFDVVEGEKGAEAANVTG PGGVPVQGSKYAA
entity_2: AACACCT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
15N chemical shifts	88
1H chemical shifts	82

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YB-1 rCSD	1
2	ssDNA	2

Entities:

Entity 1, YB-1 rCSD 93 residues - Formula weight is not available

1

GLY

PRO

MET

ASP

LYS

VAL

ILE

ALA

THR

2

LYS

VAL

LEU

GLY

THR

VAL

LYS

TRP

PHE

ASN

3

VAL

ARG

ASN

GLY

TYR

GLY

PHE

ILE

ASN

ARG

4

ASN

ASP

THR

LYS

GLU

ASP

VAL

PHE

VAL

HIS

5

GLN

THR

ALA

ILE

LYS

ASN

PRO

ARG

6

LYS

TYR

LEU

ARG

SER

VAL

GLY

ASP

GLY

GLU

7

THR

VAL

GLU

PHE

ASP

VAL

GLU

GLY

GLU

8

LYS

GLY

ALA

GLU

ALA

ASN

VAL

THR

GLY

9

PRO

GLY

VAL

PRO

VAL

GLN

GLY

SER

LYS

10

TYR

ALA

Entity 2, ssDNA 7 residues - Formula weight is not available

1

DA

DC

DA

DC

DT

Samples:

sample_1: Refolded Cold Shock Domain, [U-100% 15N], 0.3 mM; ssDNA 7.5 uM; Tris-HCl 25 mM; NaCl 50 mM

sample_conditions_1: pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

CcpNMR - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

BMRB Entry 53597