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BMRB: 17103

2L1R

The structure of the calcium-sensitizer, dfbp-o, in complex with the N-domain of troponin C and the switch region of troponin I

Authors

Robertson, I.M., Sun, Y., Li, M.X., Sykes, B.D.

Assembly

calcium-sensitizer, dfbp-o, in complex with troponin C and the switch region of troponin I

Entity

1. cNTnC (polymer, Thiol state: all free), 89 monomers, 10062.23 Da Detail

MDDIYKAAVE QLTEEQKNEF KAAFDIFVLG AEDGCISTKE LGKVMRMLGQ NPTPEELQEM IDEVDEDGSG TVDFDEFLVM MVRCMKDDS

2. cTnI(144-163) (polymer, Thiol state: not present), 20 monomers, 2214.660 Da Detail

RRVRISADAM MQALLGARAK

3. CA (non-polymer), 40.078 Da
4. dfbp-o (non-polymer, Thiol state: not present), 197.239 Da

Total weight

12514.208 Da

Max. entity weight

10062.23 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.2 %, Completeness: 71.9 %, Completeness (bb): 72.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.9 % (893 of 1242)	81.8 % (530 of 648)	57.9 % (278 of 480)	74.6 % (85 of 114)
Backbone	72.9 % (474 of 650)	94.2 % (210 of 223)	55.9 % (179 of 320)	79.4 % (85 of 107)
Sidechain	71.9 % (499 of 694)	75.3 % (320 of 425)	68.3 % (179 of 262)	0.0 % (0 of 7)
Aromatic	27.6 % (16 of 58)	55.2 % (16 of 29)	0.0 % (0 of 29)
Methyl	88.4 % (99 of 112)	100.0 % (56 of 56)	76.8 % (43 of 56)

1. cNTnC

MDDIYKAAVE QLTEEQKNEF KAAFDIFVLG AEDGCISTKE LGKVMRMLGQ NPTPEELQEM IDEVDEDGSG TVDFDEFLVM MVRCMKDDS

2. cTnI(144-163)

RRVRISADAM MQALLGARAK

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2L1R, Strand ID: A, B Detail

Release date

2010-09-07

Citation

A structural and functional perspective into the mechanism of Ca2+-sensitizers that target the cardiac troponin complex
Robertson, I.M., Sun, Y., Li, M.X., Sykes, B.D.
J. Mol. Cell. Cardiol. (2010), 49, 1031-1041, PubMed 20801130 , DOI 10.1016/j.yjmcc.2010.08.019 , Abstract

Related entities 1. cNTnC, : 3 : 96 entities Detail

Related entities 2. cTnI(144-163), : 1 : 10 : 13 : 35 entities Detail

Interaction partners 2. cTnI(144-163), : 18 interactors Detail

More details for 18 interactors identified by 9 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

4 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

5 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

6 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

7 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

9 3D 1H-15N TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

10 2D 13C, 15N Filtered NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

11 2D 13C,15N Filtered TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

12 2D 1H-19F HOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

13 3D 13C filtered, edited NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	cNTnC	[U-99% 13C; U-99% 15N]		0.5 ~ 1.0 mM
2	cTnI	natural abundance		2.0 ~ 4.0 mM
3	2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid	natural abundance		2.0 ~ 4.0 mM
4	Calcium	natural abundance		2.0 ~ 4.0 mM
5	KCl	natural abundance		100 mM
6	DTT	natural abundance		10 mM
7	Imidazole	natural abundance		10 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17103_2l1r.nef
Input source #2: Coordindates	2l1r.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)
1:65:ASP:OD2	3:1:CA:CA	unknown	unknown	n/a
1:73:ASP:OD2	3:1:CA:CA	unknown	unknown	n/a
1:69:SER:OG	3:1:CA:CA	unknown	unknown	n/a
1:76:GLU:OE1	3:1:CA:CA	unknown	unknown	n/a
1:76:GLU:OE2	3:1:CA:CA	unknown	unknown	n/a
1:71:THR:O	3:1:CA:CA	unknown	unknown	n/a
1:67:ASP:OD2	3:1:CA:CA	unknown	unknown	n/a
1:65:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:67:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:73:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	SXK	[(2',4'-difluorobiphenyl-4-yl)oxy]acetic acid	None
D	1	CA	CALCIUM ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80---------
MDDIYKAAVEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDDIYKAAVEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDS

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

----150-------160---
RRVRISADAMMQALLGARAK
||||||||||||||||||||
RRVRISADAMMQALLGARAK
--------10--------20

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	89	0	0	100.0
B	B	20	0	0	100.0

Content subtype: combined_17103_2l1r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	10		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	905		100.0 (chain: A, length: 89), 85.0 (chain: B, length: 20)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3080 (1)	noe	97.8 (chain: A, length: 89), 80.0 (chain: B, length: 20)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	125 (125)	.	75.3 (chain: A, length: 89), 40.0 (chain: B, length: 20)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 85.0%
- Total number of assignments
  - ¹H chemical shifts: 552
  - ¹³C chemical shifts: 268
  - ¹⁵N chemical shifts: 85
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- 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
  - Chain_ID: B

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 97.8%
  - Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 80.0%
- Total number of restraints: 2974
- Weight of restraints: 1.0 (2974)
- Potential type of restraints: square-well-parabolic (2974)
- Range of distance target values: 2.0, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
  - Chain_ID: D
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 75.3%
  - Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 40.0%
- Total number of restraints: 125
- Total number of restraints per polymer type: 125
- Weight of restraints: 1.0 (125)
- Potential type of restraints: square-well-parabolic (125)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ca2+-sensitizer, dfbp-o, N-domain, troponin C, troponin I