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BMRB: 25810

2N7L

NMR structure of the N-domain of troponin C bound to the switch region of troponin I and the covalent levosimendan analog i9.

Authors

Pineda Sanabria, S.E., Sykes, B.D., Robertson, I.M.

Assembly

N-domain of troponin C bound to the switch region of troponin I and the covalent levosimendan analog i9

Entity

1. N-domain of troponin C bound to the switch region of troponin I and the covalent levosimendan analog i9, entity 1 (polymer), 141 monomers, 16195.14 Da Detail

MHHHHHHGGL VPRGSMDDIY KAAVEQLTEE QKNEFKAAFD IFVLGAEDGS ISTKELGKVM RMLGQNPTPE ELQEMIDEVD EDGSGTVDFD EFLVMMVRXM KDDSENLYFQ GRRVRISADA MMQALLGARA KESLDLRAHL K

2. N-domain of troponin C bound to the switch region of troponin I and the covalent levosimendan analog i9, entity CA (non-polymer), 40.078 Da

Total weight

16235.218 Da

Max. entity weight

16195.14 Da

Entity Connection

metal coordination 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:GLU91:OE1	2:CA1:CA
2	metal coordination	sing	1:SER84:OG	2:CA1:CA
3	metal coordination	sing	1:GLU91:OE2	2:CA1:CA
4	metal coordination	sing	1:ASP80:OD1	2:CA1:CA
5	metal coordination	sing	1:THR86:O	2:CA1:CA
6	metal coordination	sing	1:ASP82:OD1	2:CA1:CA

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.5 %, Completeness: 63.6 %, Completeness (bb): 72.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	63.6 % (1022 of 1607)	64.6 % (541 of 838)	58.3 % (363 of 623)	80.8 % (118 of 146)
Backbone	72.7 % (606 of 834)	84.4 % (243 of 288)	60.1 % (246 of 409)	85.4 % (117 of 137)
Sidechain	58.6 % (529 of 902)	54.2 % (298 of 550)	67.1 % (230 of 343)	11.1 % (1 of 9)
Aromatic	3.8 % (4 of 104)	7.7 % (4 of 52)	0.0 % (0 of 52)
Methyl	84.1 % (116 of 138)	85.5 % (59 of 69)	82.6 % (57 of 69)

1. entity 1

MHHHHHHGGL VPRGSMDDIY KAAVEQLTEE QKNEFKAAFD IFVLGAEDGS ISTKELGKVM RMLGQNPTPE ELQEMIDEVD EDGSGTVDFD EFLVMMVRXM KDDSENLYFQ GRRVRISADA MMQALLGARA KESLDLRAHL K

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity_1	[U-15N]	0.65 mM
2	entity_2	[U-15N]	0.65 mM
3	potassium chloride	natural abundance	100 mM
4	imidazole	natural abundance	10 mM
5	calcium chloride	natural abundance	2 mM
6	DSS	[U-99% 2H]	0.25 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity_1	[U-13C; U-15N]	0.65 mM
8	entity_2	[U-13C; U-15N]	0.65 mM
9	potassium chloride	natural abundance	100 mM
10	imidazole	natural abundance	10 mM
11	calcium chloride	natural abundance	2 mM
12	DSS	[U-99% 2H]	0.25 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	entity_1	[U-13C; U-15N]	0.65 mM
14	entity_2	[U-13C; U-15N]	0.65 mM
15	potassium chloride	natural abundance	100 mM
16	imidazole	[U-99% 2H]	10 mM
17	calcium chloride	natural abundance	2 mM
18	DSS	[U-99% 2H]	0.25 mM

LACS Plot; CA

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

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.0 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N7L, Strand ID: C Detail

Release date

2016-07-19

Citation

Troponin C with covalently bound levosimendan analog i9 enhances contraction in cardiac muscle fibers
Pineda Sanabria, S.E., Robertson, I.M., Sun, Y., Irving, M., Sykes, B.D.
Not known

Related entities 1. N-domain of troponin C bound to the switch region of troponin I and the covalent levosimendan analog i9, entity 1, : 3 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity_1	[U-15N]	0.65 mM
2	entity_2	[U-15N]	0.65 mM
3	potassium chloride	natural abundance	100 mM
4	imidazole	natural abundance	10 mM
5	calcium chloride	natural abundance	2 mM
6	DSS	[U-99% 2H]	0.25 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity_1	[U-13C; U-15N]	0.65 mM
8	entity_2	[U-13C; U-15N]	0.65 mM
9	potassium chloride	natural abundance	100 mM
10	imidazole	natural abundance	10 mM
11	calcium chloride	natural abundance	2 mM
12	DSS	[U-99% 2H]	0.25 mM

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity_1	[U-13C; U-15N]	0.65 mM
8	entity_2	[U-13C; U-15N]	0.65 mM
9	potassium chloride	natural abundance	100 mM
10	imidazole	natural abundance	10 mM
11	calcium chloride	natural abundance	2 mM
12	DSS	[U-99% 2H]	0.25 mM

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity_1	[U-13C; U-15N]	0.65 mM
8	entity_2	[U-13C; U-15N]	0.65 mM
9	potassium chloride	natural abundance	100 mM
10	imidazole	natural abundance	10 mM
11	calcium chloride	natural abundance	2 mM
12	DSS	[U-99% 2H]	0.25 mM

5 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity_1	[U-15N]	0.65 mM
2	entity_2	[U-15N]	0.65 mM
3	potassium chloride	natural abundance	100 mM
4	imidazole	natural abundance	10 mM
5	calcium chloride	natural abundance	2 mM
6	DSS	[U-99% 2H]	0.25 mM

6 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity_1	[U-13C; U-15N]	0.65 mM
8	entity_2	[U-13C; U-15N]	0.65 mM
9	potassium chloride	natural abundance	100 mM
10	imidazole	natural abundance	10 mM
11	calcium chloride	natural abundance	2 mM
12	DSS	[U-99% 2H]	0.25 mM

7 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity_1	[U-13C; U-15N]	0.65 mM
8	entity_2	[U-13C; U-15N]	0.65 mM
9	potassium chloride	natural abundance	100 mM
10	imidazole	natural abundance	10 mM
11	calcium chloride	natural abundance	2 mM
12	DSS	[U-99% 2H]	0.25 mM

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity_1	[U-15N]	0.65 mM
2	entity_2	[U-15N]	0.65 mM
3	potassium chloride	natural abundance	100 mM
4	imidazole	natural abundance	10 mM
5	calcium chloride	natural abundance	2 mM
6	DSS	[U-99% 2H]	0.25 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	entity_1	[U-13C; U-15N]	0.65 mM
14	entity_2	[U-13C; U-15N]	0.65 mM
15	potassium chloride	natural abundance	100 mM
16	imidazole	[U-99% 2H]	10 mM
17	calcium chloride	natural abundance	2 mM
18	DSS	[U-99% 2H]	0.25 mM

10 gnoesyChsqc_CNfilt

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity_1	[U-13C; U-15N]	0.65 mM
8	entity_2	[U-13C; U-15N]	0.65 mM
9	potassium chloride	natural abundance	100 mM
10	imidazole	natural abundance	10 mM
11	calcium chloride	natural abundance	2 mM
12	DSS	[U-99% 2H]	0.25 mM

11 2D 1H-1H NOESY CN filtered

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	entity_1	[U-13C; U-15N]	0.65 mM
14	entity_2	[U-13C; U-15N]	0.65 mM
15	potassium chloride	natural abundance	100 mM
16	imidazole	[U-99% 2H]	10 mM
17	calcium chloride	natural abundance	2 mM
18	DSS	[U-99% 2H]	0.25 mM

12 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	entity_1	[U-13C; U-15N]	0.65 mM
14	entity_2	[U-13C; U-15N]	0.65 mM
15	potassium chloride	natural abundance	100 mM
16	imidazole	[U-99% 2H]	10 mM
17	calcium chloride	natural abundance	2 mM
18	DSS	[U-99% 2H]	0.25 mM

13 2D 1H-19F HMQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	entity_1	[U-13C; U-15N]	0.65 mM
14	entity_2	[U-13C; U-15N]	0.65 mM
15	potassium chloride	natural abundance	100 mM
16	imidazole	[U-99% 2H]	10 mM
17	calcium chloride	natural abundance	2 mM
18	DSS	[U-99% 2H]	0.25 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25810_2n7l.nef
Input source #2: Coordindates	2n7l.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	Warning

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)
1:98:ARG:C	1:99:4J4:N	unknown	unknown	n/a
1:99:4J4:C	1:100:MET:N	unknown	unknown	n/a
1:91:GLU:OE1	2:1:CA:CA	unknown	unknown	n/a
1:84:SER:OG	2:1:CA:CA	unknown	unknown	n/a
1:91:GLU:OE2	2:1:CA:CA	unknown	unknown	n/a
1:80:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:86:THR:O	2:1:CA:CA	unknown	unknown	n/a
1:82:ASP:OD1	2:1: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
C	84	4J4	S-(2-{[(2',4'-difluorobiphenyl-4-yl)methyl]amino}-2-oxoethyl)-L-cysteine	Assigned chemical shifts, Coordinates

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	141	0	0	100.0

Content subtype: combined_25810_2n7l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	cChimera-i9	Warning	1007		91.5 (chain: C, length: 141)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2 (1)	undefined	No information
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	2355 (1)	noe	83.7 (chain: C, length: 141)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	195 (195)	.	75.9 (chain: C, length: 141)

Assigned chemical shifts

Saveframe: cChimera-i9
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 141, Sequence coverage: 91.5%
- Total number of assignments
  - ¹³C chemical shifts: 351
  - ¹H chemical shifts: 539
  - ¹⁵N chemical shifts: 115
  - ¹⁹F chemical shifts: 2
- Completeness of assignments
  - Entity_assemble_ID: C
- 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: C

Comp_index_ID	Comp_ID
84	4J4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	623	349	56.0
¹H chemical shifts	838	531	63.4
¹⁵N chemical shifts	154	115	74.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	280	121	43.2
¹H chemical shifts	288	243	84.4
¹⁵N chemical shifts	137	115	83.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	343	228	66.5
¹H chemical shifts	550	288	52.4
¹⁵N chemical shifts	17	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	79	65	82.3
¹H chemical shifts	79	67	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	52	0	0.0
¹H chemical shifts	52	3	5.8

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: undefined
- Total number of restraints: 2
- Weight of restraints: 1.0 (2)
- Potential type of restraints: square-well-parabolic (2)
- Range of distance target values: 2.0, 2.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: C
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: C, Chain length: 141, Sequence coverage: 83.7%
  - Total number of restraints: 2270
  - Weight of restraints: 1.0 (2270)
  - Potential type of restraints: square-well-parabolic (2270)
  - Range of distance target values: 2.4, 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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 141, Sequence coverage: 75.9%
- Total number of restraints: 195
- Total number of restraints per polymer type: 195
- Weight of restraints: 1.0 (195)
- Potential type of restraints: square-well-parabolic (195)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: C

Keywords NMR, calcium sensitizer, contraction regulation, levosimendan, troponin C

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Found 1 Document (0.71 seconds)

BMRB: 25810

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. N-domain of troponin C bound to the switch region of troponin I and the covalent levosimendan analog i9, entity 1, : 3 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail