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BMRB: 15679

2K1M

3D NMR structure of domain cC0 of cardiac myosin bonding protein C (MyBP-C)

Authors

Ratti, J., Gautel, M., Pfuhl, M.

Assembly

MyBP-C

Entity

1. MyBP-C (polymer, Thiol state: not present), 95 monomers, 10029.17 Da Detail

PEPGKKPVSA FSKKPRSVEV AAGSPAVFEA ETERAGVKVR WQRGGSDISA SNKYGLATEG TRHTLTVREV GPADQGSYAV IAGSSKVKFD LKVIE

Formula weight

10029.17 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.8 %, Completeness: 85.9 %, Completeness (bb): 82.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.9 % (903 of 1051)	93.6 % (512 of 547)	73.5 % (302 of 411)	95.7 % (89 of 93)
Backbone	82.6 % (461 of 558)	95.9 % (186 of 194)	68.4 % (188 of 275)	97.8 % (87 of 89)
Sidechain	90.5 % (523 of 578)	92.4 % (326 of 353)	88.2 % (195 of 221)	50.0 % (2 of 4)
Aromatic	87.1 % (54 of 62)	100.0 % (31 of 31)	73.3 % (22 of 30)	100.0 % (1 of 1)
Methyl	98.0 % (98 of 100)	100.0 % (50 of 50)	96.0 % (48 of 50)

1. cC0 MyBPC

PEPGKKPVSA FSKKPRSVEV AAGSPAVFEA ETERAGVKVR WQRGGSDISA SNKYGLATEG TRHTLTVREV GPADQGSYAV IAGSSKVKFD LKVIE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	cC0_MyBPC	[U-95% 13C; U-95% 15N]		1-1.5 (±0.2) mM
2	D2O	[U-2H]		55.5 M
3	sodium phosphate	natural abundance		40 mM
4	sodium chloride	natural abundance		50 mM
5	DTT	natural abundance		2 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
6	cC0_MyBPC	[U-95% 15N]		1-1.5 (±0.2) mM
7	H2O	natural abundance		55.5 M
8	sodium phosphate	natural abundance		40 mM
9	sodium chloride	natural abundance		50 mM
10	DTT	natural abundance		2 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
11	cC0_MyBPC	natural abundance		1-1.5 (±0.2) mM
12	H2O	natural abundance		55.5 M
13	sodium phosphate	natural abundance		40 mM
14	sodium chloride	natural abundance		50 mM
15	DTT	natural abundance		2 mM

LACS Plot; CA

Referencing offset: 0.06 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: 0.06 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K1M, Strand ID: A Detail

Release date

2009-10-12

Citation

Structure and interactions of myosin-binding protein C domain C0: cardiac-specific regulation of myosin at its neck?
Ratti, J., Rostkova, E., Gautel, M., Pfuhl, M.
J. Biol. Chem. (2011), 286, 12650-12658, PubMed 21297165 , DOI 10.1074/jbc.M110.156646 , Abstract

Related entities 1. MyBP-C, : 1 : 4 : 345 entities Detail

Interaction partners 1. MyBP-C, : 5 interactors Detail

More details for 5 interactors identified by 4 citations

Experiments performed 10 experiments Detail

1 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	cC0_MyBPC	[U-95% 13C; U-95% 15N]		1-1.5 (±0.2) mM
2	D2O	[U-2H]		55.5 M
3	sodium phosphate	natural abundance		40 mM
4	sodium chloride	natural abundance		50 mM
5	DTT	natural abundance		2 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
6	cC0_MyBPC	[U-95% 15N]		1-1.5 (±0.2) mM
7	H2O	natural abundance		55.5 M
8	sodium phosphate	natural abundance		40 mM
9	sodium chloride	natural abundance		50 mM
10	DTT	natural abundance		2 mM

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	cC0_MyBPC	[U-95% 13C; U-95% 15N]		1-1.5 (±0.2) mM
2	D2O	[U-2H]		55.5 M
3	sodium phosphate	natural abundance		40 mM
4	sodium chloride	natural abundance		50 mM
5	DTT	natural abundance		2 mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	cC0_MyBPC	[U-95% 13C; U-95% 15N]		1-1.5 (±0.2) mM
2	D2O	[U-2H]		55.5 M
3	sodium phosphate	natural abundance		40 mM
4	sodium chloride	natural abundance		50 mM
5	DTT	natural abundance		2 mM

5 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	cC0_MyBPC	[U-95% 13C; U-95% 15N]		1-1.5 (±0.2) mM
2	D2O	[U-2H]		55.5 M
3	sodium phosphate	natural abundance		40 mM
4	sodium chloride	natural abundance		50 mM
5	DTT	natural abundance		2 mM

6 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	cC0_MyBPC	[U-95% 13C; U-95% 15N]		1-1.5 (±0.2) mM
2	D2O	[U-2H]		55.5 M
3	sodium phosphate	natural abundance		40 mM
4	sodium chloride	natural abundance		50 mM
5	DTT	natural abundance		2 mM

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
11	cC0_MyBPC	natural abundance		1-1.5 (±0.2) mM
12	H2O	natural abundance		55.5 M
13	sodium phosphate	natural abundance		40 mM
14	sodium chloride	natural abundance		50 mM
15	DTT	natural abundance		2 mM

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	cC0_MyBPC	[U-95% 13C; U-95% 15N]		1-1.5 (±0.2) mM
2	D2O	[U-2H]		55.5 M
3	sodium phosphate	natural abundance		40 mM
4	sodium chloride	natural abundance		50 mM
5	DTT	natural abundance		2 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	cC0_MyBPC	[U-95% 13C; U-95% 15N]		1-1.5 (±0.2) mM
2	D2O	[U-2H]		55.5 M
3	sodium phosphate	natural abundance		40 mM
4	sodium chloride	natural abundance		50 mM
5	DTT	natural abundance		2 mM

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
6	cC0_MyBPC	[U-95% 15N]		1-1.5 (±0.2) mM
7	H2O	natural abundance		55.5 M
8	sodium phosphate	natural abundance		40 mM
9	sodium chloride	natural abundance		50 mM
10	DTT	natural abundance		2 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15679_2k1m.nef
Input source #2: Coordindates	2k1m.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-----
PEPGKKPVSAFSKKPRSVEVAAGSPAVFEAETERAGVKVRWQRGGSDISASNKYGLATEGTRHTLTVREVGPADQGSYAVIAGSSKVKFDLKVIE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PEPGKKPVSAFSKKPRSVEVAAGSPAVFEAETERAGVKVRWQRGGSDISASNKYGLATEGTRHTLTVREVGPADQGSYAVIAGSSKVKFDLKVIE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	95	0	0	100.0

Content subtype: combined_15679_2k1m.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	873		94.7 (chain: A, length: 95)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	1518 (1)	noe	91.6 (chain: A, length: 95)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	Warning	326 (326)	.	100.0 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 94.7%
- Total number of assignments
  - ¹H chemical shifts: 507
  - ¹³C chemical shifts: 281
  - ¹⁵N chemical shifts: 85
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 91.6%
- Total number of restraints: 1495
- Weight of restraints: 1.0 (1495)
- Potential type of restraints: upper-bound-parabolic (1495)
- Range of distance target values: 2.34, 6.05 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 100.0%
- Total number of restraints: 326
- Total number of restraints per polymer type: 326
- Weight of restraints: 1.0 (326)
- Potential type of restraints: square-well-parabolic (326)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Cardiac Muscle, Hypertrophic cardiomyopathy, Ig-I domain, Myosin Binding Protein C