BMRB Entry 34988

Name: Solution structure of Sox2 DBD
Published: 2025-11-11

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PDB ID: 9qpf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34988
MolProbity Validation Chart

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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:

Solution structure of Sox2 DBD

Deposition date:

2025-03-27

Original release date:

2025-11-11

Authors:

Orsetti, A.; van Ingen, H.

Citation:

Citation: Orsetti, Andrea; Slejfer, Jonathan; Ha, Satine; Kevelam, Damian; Tekkelenburg, Jan; van Duijn, Tjitske; Leppakoski, Anni; Sedrakyan, Aren; Szilagyi, Akos; Schellevis, Raymond; Soufi, Abdenour; Cojocaru, Vlad; van Ingen, Hugo. "Solution structure of the Sox2 DNA-binding domain reveals conformational selection in DNA binding" Nucleic Acids Res 53, .-. (2025).
PubMed: 41189057

Assembly members:

Assembly members:
entity_1, polymer, 97 residues, 11771.786 Da.

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSNQKNSPDRVKRPMNAFMV WSRGQRRKMAQENPKMHNSE ISKRLGAEWKLLSETEKRPF IDEAKRLRALHMKEHPDYKY RPRRKTKTLMKKDKYTL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	423
15N chemical shifts	95
1H chemical shifts	670

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 97 residues - 11771.786 Da.

1

GLY

SER

ASN

GLN

LYS

ASN

SER

PRO

ASP

ARG

2

VAL

LYS

ARG

PRO

MET

ASN

ALA

PHE

MET

VAL

3

TRP

SER

ARG

GLY

GLN

ARG

LYS

MET

ALA

4

GLN

GLU

ASN

PRO

LYS

MET

HIS

ASN

SER

GLU

5

ILE

SER

LYS

ARG

LEU

GLY

ALA

GLU

TRP

LYS

6

LEU

SER

GLU

THR

GLU

LYS

ARG

PRO

PHE

7

ILE

ASP

GLU

ALA

LYS

ARG

LEU

ARG

ALA

LEU

8

HIS

MET

LYS

GLU

HIS

PRO

ASP

TYR

LYS

TYR

9

ARG

PRO

ARG

LYS

THR

LYS

THR

LEU

MET

10

LYS

ASP

LYS

TYR

THR

LEU

Samples:

sample_1: Sox2-DBD, [U-13C; U-15N], 0.25 mM; potassium chloride 135 mM; TRIS 20 mM; sodium chloride 15 mM; sodium azide 0.01 % v/v

sample_2: Sox2-DBD, [U-13C; U-15N], 0.25 mM; potassium chloride 135 mM; TRIS 20 mM; sodium chloride 15 mM; sodium azide 0.01 % v/v; pentaethylene glycol monodecyl/n-Hexanol 5 % v/v

sample_conditions_1: ionic strength: 150 mM; pH: 7.30; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	anisotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.98.15, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure calculation

Poky, Manthey, Tonelli, Clos II, Rahimi, Markley and Lee - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker AVANCE NEO 1200 MHz
Bruker AVANCE NEO 900 MHz
Bruker AVANCE III 600 MHz
Bruker AVANCE III 850 MHz

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