BMRB Entry 16680

Name: Solution structure of human stem cell transcription factor Nanog
Published: 2012-08-03

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PDB ID: 2kt0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16680
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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 human stem cell transcription factor Nanog

Deposition date:

2010-01-15

Original release date:

2012-08-03

Authors:

Sahu, S.; Markley, J.

Citation:

Citation: Sahu, S.; Markley, J.. "Solution structure of human stem cell transcription factor Nanog" To be published ., .-..

Assembly members:

Assembly members:
Nanog, polymer, 84 residues, 10068.668 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: pVP68K

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Nanog: SKQPTSAENSVAKKEDKVPV KKQKTRTVFSSTQLCVLNDR FQRQKYLSLQQMQELSNILN LSYKQVKTWFQNQRMKSKRW QKNN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	396
15N chemical shifts	81
1H chemical shifts	651

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Nanog	1

Entities:

Entity 1, Nanog 84 residues - 10068.668 Da.

1

SER

LYS

GLN

PRO

THR

SER

ALA

GLU

ASN

SER

2

VAL

ALA

LYS

GLU

ASP

LYS

VAL

PRO

VAL

3

LYS

GLN

LYS

THR

ARG

THR

VAL

PHE

SER

4

SER

THR

GLN

LEU

CYS

VAL

LEU

ASN

ASP

ARG

5

PHE

GLN

ARG

GLN

LYS

TYR

LEU

SER

LEU

GLN

6

GLN

MET

GLN

GLU

LEU

SER

ASN

ILE

LEU

ASN

7

LEU

SER

TYR

LYS

GLN

VAL

LYS

THR

TRP

PHE

8

GLN

ASN

GLN

ARG

MET

LYS

SER

LYS

ARG

TRP

9

GLN

LYS

ASN

Samples:

sample_1: Nanog, [U-95% 13C; U-90% 15N], 0.7 mM; MOPS 10 mM; Dithiothreitol 5 mM; NaCl 250 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 250 mM; pH: 7.0; 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 v1.21, Brunger A. T. et.al. - refinement

NMR spectrometers:

Varian Inova 600 MHz

PDB	2KT0 4RBO
DBJ	BAB14151 BAC76999 BAF83585
GB	AAI60187 AAP49529 AAT81526 ABA27089 ABZ92376
REF	NP_001065295 NP_001284627 NP_079141 XP_003811843 XP_011519152
SP	Q3LTE0 Q6NSW7 Q9H9S0
AlphaFold	Q3LTE0 Q6NSW7 Q9H9S0