BMRB Entry 17691

Name: Solution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2
Published: 2011-07-06

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PDB ID: 2le4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17691
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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 the HMG box DNA-binding domain of human stem cell transcription factor Sox2

Deposition date:

2011-06-06

Original release date:

2011-07-06

Authors:

Sahu, Sarata; Markley, John; Tonelli, Marco; Bahrami, Arash; Eghbalnia, Hamid

Citation:

Citation: Sahu, Sarata; Markley, John; Tonelli, Marco; Bahrami, Arash; Eghbalnia, Hamid. "Not known" .

Assembly members:

Assembly members:
Sox2, polymer, 81 residues, 9920.689 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 Vector: pEU-HIS

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Sox2: SDRVKRPMNAFMVWSRGQRR KMAQENPKMHNSEISKRLGA EWKLLSETEKRPFIDEAKRL RALHMKEHPDYKYRPRRKTK T

Data sets:

assigned_chemical_shifts
- sox2Asn

Data type	Count
13C chemical shifts	370
15N chemical shifts	80
1H chemical shifts	532

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Sox2	1

Entities:

Entity 1, Sox2 81 residues - 9920.689 Da.

1

SER

ASP

ARG

VAL

LYS

ARG

PRO

MET

ASN

ALA

2

PHE

MET

VAL

TRP

SER

ARG

GLY

GLN

ARG

3

LYS

MET

ALA

GLN

GLU

ASN

PRO

LYS

MET

HIS

4

ASN

SER

GLU

ILE

SER

LYS

ARG

LEU

GLY

ALA

5

GLU

TRP

LYS

LEU

SER

GLU

THR

GLU

LYS

6

ARG

PRO

PHE

ILE

ASP

GLU

ALA

LYS

ARG

LEU

7

ARG

ALA

LEU

HIS

MET

LYS

GLU

HIS

PRO

ASP

8

TYR

LYS

TYR

ARG

PRO

ARG

LYS

THR

LYS

9

THR

Samples:

sample_1: Sox2, [U-100% 13C; U-100% 15N], 0.7 ± 0.02 mM; DTT 5 ± 0.05 %; MOPS 10 mM; NaCl 100 mM; H20 95%; D20 5%

sample_conditions_1: ionic strength: 100 mM; pH: 6.7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D_15N-separated_NOESY	sample_1	isotropic	sample_conditions_1
3D_13C-separated_NOESY	sample_1	isotropic	sample_conditions_1
3D_13C-separated_NOESY (AROMATIC)	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

NMR spectrometers:

Varian Inova 600 MHz

PDB	1GT0 1O4X 2LE4
DBJ	BAA09168 BAC55017 BAC67545 BAC75668 BAE20882
EMBL	CAA63847 CAA65725 CAA80631 CAA83435 CAF91617
GB	AAA35997 AAB09662 AAB62821 AAC14215 AAC31791
PRF	1612347C
REF	NP_001081691 NP_001098933 NP_001102651 NP_001116669 NP_001135190
SP	O42569 P48430 P48431 P48432 P54231
TPG	DAA33313
AlphaFold	O42569 P48430 P48431 P48432 P54231