BMRB Entry 51417

Name: Bromodomain Interactions with Acetylated Histone 4 Peptides in the Tandem Domain BRD4 -- Effects on Domain Dynamics and Internal Flexibility
Published: 2022-10-11

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51417

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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: Bromodomain Interactions with Acetylated Histone 4 Peptides in the Tandem Domain BRD4 -- Effects on Domain Dynamics and Internal Flexibility PubMed: 36215732

Deposition date: 2022-04-26 Original release date: 2022-10-11

Authors: Wernersson, Sven; Romel, Bobby; Flavell, Liz; Milbradt, Alexander; Holdgate, Geoff; Embrey, Kevin; Akke, Mikael

Citation: Wernersson, Sven; Bobby, Romel; Flavell, Liz; Milbradt, Alexander; Holdgate, Geoffrey; Embrey, Kevin; Akke, Mikael. "Bromodomain Interactions with Acetylated Histone 4 Peptides in the BRD4 Tandem Domain: Effects on Domain Dynamics and Internal Flexibility" Biochemistry 61, 2303-2318 (2022).

Assembly members:
entity_1, polymer, 120 residues, Formula weight is not available

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

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28

Entity Sequences (FASTA):
entity_1: HPAPEKSSKVSEQLKCCSGI LKEMFAKKHAAYAWPFYKPV DVEALGLHDYCDIIKHPMDM STIKSKLEAREYRDAQEFGA DVRLMFSNCYKYNPPDHEVV AMARKLQDVFEMRFAKMPDE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
heteronucl_NOEs
- heteronucl_NOEs_1
- heteronucl_NOEs_2
heteronucl_T1_relaxation
- heteronucl_T1_relaxation_1
- heteronucl_T1_relaxation_2
heteronucl_T2_relaxation
- heteronucl_T2_relaxation_1
- heteronucl_T2_relaxation_2
order_parameters
- order_parameters_1

Data type	Count
15N chemical shifts	104
1H chemical shifts	104
T1 relaxation values	180
T2 relaxation values	180
dipole-CSA cross correlation relaxation values	87
heteronuclear NOE values	180
order parameters	90

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	BD2	1

Entities:

Entity 1, BD2 120 residues - Formula weight is not available

1	HIS	PRO	ALA	PRO	GLU	LYS	SER	SER	LYS	VAL
2	SER	GLU	GLN	LEU	LYS	CYS	CYS	SER	GLY	ILE
3	LEU	LYS	GLU	MET	PHE	ALA	LYS	LYS	HIS	ALA
4	ALA	TYR	ALA	TRP	PRO	PHE	TYR	LYS	PRO	VAL
5	ASP	VAL	GLU	ALA	LEU	GLY	LEU	HIS	ASP	TYR
6	CYS	ASP	ILE	ILE	LYS	HIS	PRO	MET	ASP	MET
7	SER	THR	ILE	LYS	SER	LYS	LEU	GLU	ALA	ARG
8	GLU	TYR	ARG	ASP	ALA	GLN	GLU	PHE	GLY	ALA
9	ASP	VAL	ARG	LEU	MET	PHE	SER	ASN	CYS	TYR
10	LYS	TYR	ASN	PRO	PRO	ASP	HIS	GLU	VAL	VAL
11	ALA	MET	ALA	ARG	LYS	LEU	GLN	ASP	VAL	PHE
12	GLU	MET	ARG	PHE	ALA	LYS	MET	PRO	ASP	GLU

Samples:

sample_1: apo Bromodomain 1 (BD1) of BRD4, [U-100% 13C; U-100% 15N], 0.135 mM; sodium phosphate 20 mM; sodium chloride 100 mM; TCEP 1 mM

sample_conditions_1: ionic strength: 0.180 M; pH: 6.8; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D CBCANH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe	sample_1	isotropic	sample_conditions_1
transverse cross-correlated dipole/CSA relaxation	sample_1	isotropic	sample_conditions_1

Software:

CcpNMR - chemical shift assignment

NMRPipe - processing

Relax - data analysis

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker Avance 600 MHz

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

1	HIS	PRO	ALA	PRO	GLU	LYS	SER	SER	LYS	VAL
2	SER	GLU	GLN	LEU	LYS	CYS	CYS	SER	GLY	ILE
3	LEU	LYS	GLU	MET	PHE	ALA	LYS	LYS	HIS	ALA
4	ALA	TYR	ALA	TRP	PRO	PHE	TYR	LYS	PRO	VAL
5	ASP	VAL	GLU	ALA	LEU	GLY	LEU	HIS	ASP	TYR
6	CYS	ASP	ILE	ILE	LYS	HIS	PRO	MET	ASP	MET
7	SER	THR	ILE	LYS	SER	LYS	LEU	GLU	ALA	ARG
8	GLU	TYR	ARG	ASP	ALA	GLN	GLU	PHE	GLY	ALA
9	ASP	VAL	ARG	LEU	MET	PHE	SER	ASN	CYS	TYR
10	LYS	TYR	ASN	PRO	PRO	ASP	HIS	GLU	VAL	VAL
11	ALA	MET	ALA	ARG	LYS	LEU	GLN	ASP	VAL	PHE
12	GLU	MET	ARG	PHE	ALA	LYS	MET	PRO	ASP	GLU

1	HIS	PRO	ALA	PRO	GLU	LYS	SER	SER	LYS	VAL
2	SER	GLU	GLN	LEU	LYS	CYS	CYS	SER	GLY	ILE
3	LEU	LYS	GLU	MET	PHE	ALA	LYS	LYS	HIS	ALA
4	ALA	TYR	ALA	TRP	PRO	PHE	TYR	LYS	PRO	VAL
5	ASP	VAL	GLU	ALA	LEU	GLY	LEU	HIS	ASP	TYR
6	CYS	ASP	ILE	ILE	LYS	HIS	PRO	MET	ASP	MET
7	SER	THR	ILE	LYS	SER	LYS	LEU	GLU	ALA	ARG
8	GLU	TYR	ARG	ASP	ALA	GLN	GLU	PHE	GLY	ALA
9	ASP	VAL	ARG	LEU	MET	PHE	SER	ASN	CYS	TYR
10	LYS	TYR	ASN	PRO	PRO	ASP	HIS	GLU	VAL	VAL
11	ALA	MET	ALA	ARG	LYS	LEU	GLN	ASP	VAL	PHE
12	GLU	MET	ARG	PHE	ALA	LYS	MET	PRO	ASP	GLU

1	HIS	PRO	ALA	PRO	GLU	LYS	SER	SER	LYS	VAL
2	SER	GLU	GLN	LEU	LYS	CYS	CYS	SER	GLY	ILE
3	LEU	LYS	GLU	MET	PHE	ALA	LYS	LYS	HIS	ALA
4	ALA	TYR	ALA	TRP	PRO	PHE	TYR	LYS	PRO	VAL
5	ASP	VAL	GLU	ALA	LEU	GLY	LEU	HIS	ASP	TYR
6	CYS	ASP	ILE	ILE	LYS	HIS	PRO	MET	ASP	MET
7	SER	THR	ILE	LYS	SER	LYS	LEU	GLU	ALA	ARG
8	GLU	TYR	ARG	ASP	ALA	GLN	GLU	PHE	GLY	ALA
9	ASP	VAL	ARG	LEU	MET	PHE	SER	ASN	CYS	TYR
10	LYS	TYR	ASN	PRO	PRO	ASP	HIS	GLU	VAL	VAL
11	ALA	MET	ALA	ARG	LYS	LEU	GLN	ASP	VAL	PHE
12	GLU	MET	ARG	PHE	ALA	LYS	MET	PRO	ASP	GLU