BMRB Entry 50873

Name: Structural description of DNA target search by a disordered transcription factor
Published: 2024-08-28

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50873

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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:

Structural description of DNA target search by a disordered transcription factor

Deposition date:

2021-04-07

Original release date:

2024-08-28

Authors:

Kelly, Conor Francis; Redfield, Christina; Shammas, Sarah

Citation:

Citation: Kelly, Conor Francis; Kuravsky, Mikhail; Redfield, Christina; Shammas, Sarah. "The transition state for coupled folding and binding of a disordered DNA binding domain resembles the unbound state" Nucleic Acids Res. ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 56 residues, Formula weight is not available
entity_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: pHSG299

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GKREVRLMKNREAARESRRK KKEYVKSLENRVAVLENQNK TLIEELKALKDLYSHK
entity_2: AGATGACGTCATCT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	197
15N chemical shifts	57
1H chemical shifts	231

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CREB 285-339, chain 1	1
2	CREB 285-339, chain 2	1
3	CRE DNA	2

Entities:

Entity 1, CREB 285-339, chain 1 56 residues - Formula weight is not available

1

GLY

LYS

ARG

GLU

VAL

ARG

LEU

MET

LYS

ASN

2

ARG

GLU

ALA

ARG

GLU

SER

ARG

LYS

3

LYS

GLU

TYR

VAL

LYS

SER

LEU

GLU

ASN

4

ARG

VAL

ALA

VAL

LEU

GLU

ASN

GLN

ASN

LYS

5

THR

LEU

ILE

GLU

LEU

LYS

ALA

LEU

LYS

6

ASP

LEU

TYR

SER

HIS

LYS

Entity 2, CRE DNA 14 residues - Formula weight is not available

1

DA

DG

DA

DT

DG

DA

DC

DG

DT

DC

2

DA

DT

DC

DT

Samples:

sample_1: CREB 285-339 dimer, [U-98% 15N], 500 uM; Magnesium chloride 10 mM; DSS 10 uM; sodium azide 1 mM; sodium chloride 150 mM; TRIS, [U-2H], 10 mM; CRE DNA 1000 mM

sample_conditions_1: ionic strength: 0.185 M; pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HBHA(CBCACO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v3.2 - collection

NMRPipe v9.8 - data analysis

ANALYSIS v2.4.2 - chemical shift assignment

istHMS vv211_64b - processing

NMR spectrometers:

Bruker AVANCE III 750 MHz

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