BMRB Entry 30308

Name: NMR structure of the N-domain of troponin C bound to switch region of troponin I and 3-methyldiphenylamine
Published: 2017-07-10

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PDB ID: 5w88
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30308
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of the N-domain of troponin C bound to switch region of troponin I and 3-methyldiphenylamine PubMed: 27825981

Deposition date: 2017-06-30 Original release date: 2017-07-10

Authors: Cai, F.; Hwang, P.; Sykes, B.

Citation: Cai, F.; Li, M.; Pineda-Sanabria, S.; Gelozia, S.; Lindert, S.; West, F.; Sykes, B.; Hwang, P.. "Structures reveal details of small molecule binding to cardiac troponin." J. Mol. Cell. Cardiol. 101, 134-144 (2016).

Assembly members:
entity_1, polymer, 120 residues, 13495.394 Da.
entity_9XG, non-polymer, 183.249 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

Entity Sequences (FASTA):
entity_1: MDDIYKAAVEQLTEEQKNEF KAAFDIFVLGAEDGSISTKE LGKVMRMLGQNPTPEELQEM IDEVDEDGSGTVDFDEFLVM MVRSMKDDSKGKFKRPTLRR VRISADAMMQALLGARAKGH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	505
15N chemical shifts	111
1H chemical shifts	804

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_1 120 residues - 13495.394 Da.

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

Entity 2, entity_2 - C13 H13 N - 183.249 Da.

1

9XG

Samples:

sample_1: 3-methyldiphenylamine 0.5 mM; DSS, [U-99% 2H], 0.25 mM; cChimera_protein, [U-15N], 0.25 ± 0.05 mM; calcium chloride 10 mM; imidazole 10 mM; potassium chloride 100 mM

sample_2: 3-methyldiphenylamine 0.8 mM; DSS, [U-99% 2H], 0.25 mM; cChimera_protein, [U-13C; U-15N], 0.5 ± 0.1 mM; calcium chloride 10 mM; imidazole 10 mM; potassium chloride 100 mM

sample_3: 3-methyldiphenylamine 0.8 mM; DSS, [U-99% 2H], 0.25 mM; cChimera_protein, [U-13C; U-15N], 0.5 ± 0.1 mM; calcium chloride 10 mM; imidazole, [U-99% 2H], 10 mM; potassium chloride 100 mM

sample_4: 3-methyldiphenylamine 0.8 mM; DSS, [U-99% 2H], 0.25 mM; cChimera_protein, [U-10% 13C; U-100% 15N], 0.5 ± 0.1 mM; calcium chloride 10 mM; imidazole 10 mM; potassium chloride 100 mM

sample_conditions_1: pH: 6.8; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCACO	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
2D 13C,15N-double-filtered NOESY	sample_3	isotropic	sample_conditions_1
3D 13C-filtered NOESY	sample_3	isotropic	sample_conditions_1

Software:

ARIA2, Linge, O'Donoghue and Nilges - refinement, structure calculation

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

NMRViewJ, Johnson, One Moon Scientific - chemical shift assignment, peak picking

VNMRJ, Varian - collection

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 800 MHz

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

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

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

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