BMRB Entry 19511

Name: NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens solved in the presence of the DNA sequence CGACTAATTAGTCG
Published: 2013-09-30

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PDB ID: 2me0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19511
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens solved in the presence of the DNA sequence CGACTAATTAGTCG

Deposition date:

2013-09-20

Original release date:

2013-09-30

Authors:

Proudfoot, Andrew; Serrano, Pedro; Geralt, Michael; Wuthrich, Kurt

Citation:

Citation: Proudfoot, Andrew; Geralt, Michael; Elsliger, Marc-Andre; Wilson, Ian; Wuthrich, Kurt; Serrano, Pedro. "Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding" Structure 24, 1372-1379 (2016).
PubMed: 27396829

Assembly members:

Assembly members:
Gbx1, polymer, 71 residues, 8346.782 Da.
DNA_1, polymer, 14 residues, Formula weight is not available
DNA_2, 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: PET46

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Gbx1: SAPGGKSRRRRTAFTSEQLL ELEKEFHCKKYLSLTERSQI AHALKLSEVQVKIWFQNRRA KWKRIKAGNVS
DNA_1: CGACTAATTAGTCG
DNA_2: CGACTAATTAGTCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	248
15N chemical shifts	75
1H chemical shifts	493

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	homeodomain transcription factor Gbx1	1
2	DNA_1	2
3	DNA_2	3

Entities:

Entity 1, homeodomain transcription factor Gbx1 71 residues - 8346.782 Da.

1

SER

ALA

PRO

GLY

LYS

SER

ARG

2

ARG

THR

ALA

PHE

THR

SER

GLU

GLN

LEU

3

GLU

LEU

GLU

LYS

GLU

PHE

HIS

CYS

LYS

4

TYR

LEU

SER

LEU

THR

GLU

ARG

SER

GLN

ILE

5

ALA

HIS

ALA

LEU

LYS

LEU

SER

GLU

VAL

GLN

6

VAL

LYS

ILE

TRP

PHE

GLN

ASN

ARG

ALA

7

LYS

TRP

LYS

ARG

ILE

LYS

ALA

GLY

ASN

VAL

8

SER

Entity 2, DNA_1 14 residues - Formula weight is not available

1

DC

DG

DA

DC

DT

DA

DT

DA

2

DG

DT

DC

DG

Entity 3, DNA_2 14 residues - Formula weight is not available

1

DC

DG

DA

DC

DT

DA

DT

DA

2

DG

DT

DC

DG

Samples:

sample_1: Gbx1, [U-98% 13C; U-98% 15N], 0.8 mM; sodium chloride 50 mM; sodium phosphate 20 mM; sodium azide 5 mM; DNA_1 0.8 mM; DNA_2 0.8 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.220 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
APSY 4D-HACANH	sample_1	isotropic	sample_conditions_1
APSY 5D-CBCACONH	sample_1	isotropic	sample_conditions_1
APSY 5D-HACACONH	sample_1	isotropic	sample_conditions_1

Software:

CYANA, G ntert P., Keller and Wuthrich - chemical shift assignment, refinement

Opalp, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

UNIO, Herrmann and Wuthrich - chemical shift assignment, structure solution

TOPSPIN, Bruker Biospin - collection, processing

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

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