BMRB Entry 51312

Name: Assigned backbone amide and methyl chemical shifts for human Sox2 HMG domain bound to DNA containing the Fgf4 motif
Published: 2023-03-20

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51312

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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:

Assigned backbone amide and methyl chemical shifts for human Sox2 HMG domain bound to DNA containing the Fgf4 motif

Deposition date:

2022-02-07

Original release date:

2023-03-20

Authors:

Malaga Gadea, Fabiana; Nikolova, Evgenia

Citation:

Citation: Malaga Gadea, Fabiana; Nikolova, Evgenia. "Structural Plasticity of Pioneer Factor Sox2 and DNA Bendability Modulate Nucleosome Engagement and Sox2-Oct4 Synergism" J. Mol. Biol. 435, 167916-167916 (2023).
PubMed: 36495920

Assembly members:

Assembly members:
entity_1, polymer, 82 residues, Formula weight is not available
entity_2, polymer, 14 residues, Formula weight is not available
entity_3, polymer, 14 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: pET15

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPDRVKRPMNAFMVWSRGQR RKMAQENPKMHNSEISKRLG AEWKLLSETEKRPFIDEAKR LRALHMKEHPDYKYRPRRKT KT
entity_2: GACTCTTTGTTTGG
entity_3: CCAAACAAAGAGTC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	28
15N chemical shifts	73
1H chemical shifts	157

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Sox2 HMG	1
2	DNA_strand_1	2
3	DNA_strand_2	3

Entities:

Entity 1, Sox2 HMG 82 residues - Formula weight is not available

1

GLY

PRO

ASP

ARG

VAL

LYS

ARG

PRO

MET

ASN

2

ALA

PHE

MET

VAL

TRP

SER

ARG

GLY

GLN

ARG

3

ARG

LYS

MET

ALA

GLN

GLU

ASN

PRO

LYS

MET

4

HIS

ASN

SER

GLU

ILE

SER

LYS

ARG

LEU

GLY

5

ALA

GLU

TRP

LYS

LEU

SER

GLU

THR

GLU

6

LYS

ARG

PRO

PHE

ILE

ASP

GLU

ALA

LYS

ARG

7

LEU

ARG

ALA

LEU

HIS

MET

LYS

GLU

HIS

PRO

8

ASP

TYR

LYS

TYR

ARG

PRO

ARG

LYS

THR

9

LYS

THR

Entity 2, DNA_strand_1 14 residues - Formula weight is not available

1

DG

DA

DC

DT

DC

DT

DG

DT

2

DT

DG

Entity 3, DNA_strand_2 14 residues - Formula weight is not available

1

DC

DA

DC

DA

DG

2

DA

DG

DT

DC

Samples:

sample_1: Sox2, [U-13C; U-15N], 0.45 mM; DNA-Fgf4 0.5 mM; DNA-Fgf4 0.5 mM; Tris-HCl 20 mM; NaCl 25 mM; TCEP 0.5 mM; EDTA 1 mM

sample_conditions_1: ionic strength: 0.025 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D (H)CC(CO)NH TOCSY	sample_1	isotropic	sample_conditions_1
3D H(CCCO)NH TOCSY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN - data collection

NMRPipe - data processing

NESTA-NMR - data processing

SPARKY - data analysis

NMR spectrometers:

Bruker Avance 600 MHz MHz

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