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Found 1 Document (2.262 seconds)

BMRB: 19817

2MLF

NMR structure of the dilated cardiomyopathy mutation G159D in troponin C bound to the anchoring region of troponin I

Authors

Baryshnikova, O.K., Robertson, I.M., Mercier, P., Sykes, B.D.

Assembly

mutation G159D in troponin C bound to the anchoring region of troponin I

Entity

1. cCTnC (polymer, Thiol state: not present), 72 monomers, 8419.171 Da Detail

MGKSEEELSD LFRMFDKNAD GYIDLDELKI MLQATGETIT EDDIEELMKD GDKNNDGRID YDEFLEFMKD VE

2. CALCIUM ION (non-polymer), 40.078 × 2 Da

Total weight

8499.327 Da

Max. entity weight

8419.171 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.2 %, Completeness (bb): 83.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.2 % (673 of 839)	84.1 % (369 of 439)	70.7 % (229 of 324)	98.7 % (75 of 76)
Backbone	83.1 % (359 of 432)	96.0 % (143 of 149)	68.7 % (145 of 211)	98.6 % (71 of 72)
Sidechain	80.4 % (381 of 474)	77.9 % (226 of 290)	83.9 % (151 of 180)	100.0 % (4 of 4)
Aromatic	33.9 % (19 of 56)	57.1 % (16 of 28)	10.7 % (3 of 28)
Methyl	96.8 % (60 of 62)	96.8 % (30 of 31)	96.8 % (30 of 31)

1. cCTnC

MGKSEEELSD LFRMFDKNAD GYIDLDELKI MLQATGETIT EDDIEELMKD GDKNNDGRID YDEFLEFMKD VE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
10	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
11	Calcium	natural abundance	2 mM
12	DSS	natural abundance	0.2 mM
13	potassium chloride	natural abundance	100 mM
14	sodium azide	natural abundance	5 mM
15	imidazole	natural abundance	0.5 mM
16	troponin I(34-71)	natural abundance	1.2 mM
17	imidazole	[U-2H]	9.5 mM
18	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MLF, Strand ID: C Detail

Release date

2014-03-09

Citation

The dilated cardiomyopathy G159D mutation in cardiac troponin C weakens the anchoring interaction with troponin I
Baryshnikova, O.K., Robertson, I.M., Mercier, P., Sykes, B.D.
Biochemistry (2008), 47, 10950-10960, PubMed 18803402 , DOI 10.1021/bi801165c , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 19816 released on 2014-03-09
Title NMR structure of the C-domain of troponin C bound to the anchoring region of troponin I

Related entities 1. cCTnC, : 1 : 16 : 488 entities Detail

Interaction partners 1. cCTnC, : 8 interactors Detail

More details for 8 interactors identified by 5 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

2 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

4 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

5 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

6 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

7 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

9 3D 1H-15N TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

10 3D HNHA

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

11 3D HNHB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

12 2D DQF-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
10	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
11	Calcium	natural abundance	2 mM
12	DSS	natural abundance	0.2 mM
13	potassium chloride	natural abundance	100 mM
14	sodium azide	natural abundance	5 mM
15	imidazole	natural abundance	0.5 mM
16	troponin I(34-71)	natural abundance	1.2 mM
17	imidazole	[U-2H]	9.5 mM
18	D2O	natural abundance	100 %

13 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
10	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
11	Calcium	natural abundance	2 mM
12	DSS	natural abundance	0.2 mM
13	potassium chloride	natural abundance	100 mM
14	sodium azide	natural abundance	5 mM
15	imidazole	natural abundance	0.5 mM
16	troponin I(34-71)	natural abundance	1.2 mM
17	imidazole	[U-2H]	9.5 mM
18	D2O	natural abundance	100 %

14 2D 13C-15N Filtered 1H-1H TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

15 2D 13C-15N Filtered 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

16 2D 13C Edited,Filtered NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.7

#	Name	Isotope labeling	Concentration
1	cCTnC	[U-95% 13C; U-95% 15N]	0.5 mM
2	Calcium	natural abundance	2 mM
3	DSS	natural abundance	0.2 mM
4	potassium chloride	natural abundance	100 mM
5	sodium azide	natural abundance	5 mM
6	imidazole	natural abundance	10 mM
7	troponin I(34-71)	natural abundance	1.2 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19817_2mlf.nef
Input source #2: Coordindates	2mlf.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:16:ASP:OD2	2:2:CA:CA	unknown	unknown	n/a
1:63:GLU:OE1	2:1:CA:CA	unknown	unknown	n/a
1:20:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:27:GLU:OE2	2:2:CA:CA	unknown	unknown	n/a
1:56:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:20:ASP:OD2	2:2:CA:CA	unknown	unknown	n/a
1:27:GLU:OE1	2:2:CA:CA	unknown	unknown	n/a
1:56:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:58:ARG:O	2:1:CA:CA	unknown	unknown	n/a
1:63:GLU:OE2	2:1:CA:CA	unknown	unknown	n/a
1:52:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:16:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	CA	CALCIUM ION	None
A	2	CA	CALCIUM ION	None

Sequence alignments

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
C	C	72	0	0	100.0

Content subtype: combined_19817_2mlf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	12		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	666		100.0 (chain: C, length: 72)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Error	1479 (1)	noe	98.6 (chain: C, length: 72)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Warning	72 (66)	.	61.1 (chain: C, length: 72)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 72, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 371
  - ¹³C chemical shifts: 220
  - ¹⁵N chemical shifts: 75
- Completeness of assignments
  - Entity_assemble_ID: C
- 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: C

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	439	370	84.3
¹³C chemical shifts	324	219	67.6
¹⁵N chemical shifts	78	75	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	145	97.3
¹³C chemical shifts	144	71	49.3
¹⁵N chemical shifts	72	71	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	290	225	77.6
¹³C chemical shifts	180	148	82.2
¹⁵N chemical shifts	6	4	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	34	94.4
¹³C chemical shifts	36	34	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	15	53.6
¹³C chemical shifts	28	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 72, Sequence coverage: 98.6%
- Total number of restraints: 1469
- Weight of restraints: 1.0 (1469)
- Potential type of restraints: square-well-parabolic (1469)
- Range of distance target values: 2.75, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: C
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 72, Sequence coverage: 61.1%
- Total number of restraints: 66
- Total number of restraints per polymer type: 66
- Weight of restraints: 1.0 (66)
- Potential type of restraints: square-well-parabolic (66)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: C

Keywords troponin C, metal binding protein, dilated cardiomyopathy, G159D, EF-hand

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Found 1 Document (2.262 seconds)

BMRB: 19817

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. cCTnC, : 1 : 16 : 488 entities Detail

Interaction partners 1. cCTnC, : 8 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail