BMRB Entry 30484

Name: NMR structure for Sp1 transcription factor duplex 5'-d(GGGGCGGGA)
Published: 2019-06-26

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30484

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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 for Sp1 transcription factor duplex 5'-d(GGGGCGGGA)

Deposition date: 2018-06-25 Original release date: 2019-06-26

Authors: Davis, E.; Hennig, M.; Arya, D.

Citation: Davis, E.; Hennig, M.; Arya, D.. "An NMR Structure Determination and Analysis of Four Sp1 Consensus Sequences" . ., .-..

Assembly members:
entity_1, polymer, 9 residues, 2861.872 Da.
entity_2, polymer, 9 residues, 2612.714 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGGGCGGGA
entity_2: TCCCGCCCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
1H chemical shifts	138

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 9 residues - 2861.872 Da.

1

DG

DC

DG

DA

Entity 2, entity_2 9 residues - 2612.714 Da.

1

DT

DC

DG

DC

Samples:

sample_1: entity_1 1.0 mM; entity_2 1.0 mM; NaCl 25 mM; Na Phosphate 5 mM; EDTA 0.5 mM

sample_2: entity_1 810 uM; entity_2 810 uM; NaCl 25 mM; Na Phosphate 5 mM; EDTA 0.5 mM

sample_conditions_1: ionic strength: 30 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D ECOSY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

AMBER v14.0, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

SPARKY, Goddard - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

3DNA, Lu - data analysis

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 800 MHz
Bruker AvanceIII 850 MHz