BMRB Entry 50251

Name: Heme-bound REV-ERBb ligand binding domain (LBD)
Published: 2021-12-15

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50251

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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: Heme-bound REV-ERBb ligand binding domain (LBD) PubMed: 33571111

Deposition date: 2020-04-29 Original release date: 2021-12-15

Authors: Mosure, Sarah; Kojetin, Douglas

Citation: Mosure, Sarah; Strutzenberg, Timothy; Shang, Jinsai; Munoz-Tello, Paola; Solt, Laura; Griffin, Patrick; Kojetin, Douglas. "Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERBb" Sci. Adv. 7, eabc6479-eabc6479 (2021).

Assembly members:
entity_1, polymer, 200 residues, Formula weight is not available
entity_HEM, non-polymer, 616.487 Da.

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: pET46

Entity Sequences (FASTA):
entity_1: GPHLVCPMSKSPYVDPHKSG HEIWEEFSMSFTPAVKEVVE FAKRIPGFRDLSQHDQVNLL KAGTFEVLMVRFASLFDAKE RTVTFLSGKKYSVDDLHSMG AGDLLNSMFEFSEKLNALQL SDEEMSLFTAVVLVSADRSG IENVNSVEALQETLIRALRT LIMKNHPNEASIFTKLLLKL PDLRSLNNMHSEELLAFKVH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	283
15N chemical shifts	90
1H chemical shifts	90

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	LBD	1
2	Heme	2

Entities:

Entity 1, LBD 200 residues - Formula weight is not available

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

Entity 2, Heme - C34 H32 Fe N4 O4 - 616.487 Da.

1

HEM

Samples:

sample_1: REV-ERBb LBD, [U-100% 13C; U-100% 15N; U-80% 2H], 1 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 1H	sample_1	isotropic	sample_conditions_1
2D TROSY 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D TROSY-HNCO	sample_1	isotropic	sample_conditions_1
3D TROSY-HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D TROSY-HNCA	sample_1	isotropic	sample_conditions_1
3D TROSY-HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D TROSY-HN(CA)CB	sample_1	isotropic	sample_conditions_1
3D TROSY-HN(COCA)CB	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v3 - collection

NMRFx Processor v10.3 - processing

NMRViewJ v9.2 - chemical shift calculation, peak picking

NMR spectrometers:

Bruker Avance 700 MHz

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

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

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

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