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BMRB: 17264

2L53

Solution NMR Structure of apo-calmodulin in complex with the IQ motif of Human Cardiac Sodium Channel NaV1.5

Authors

Chagot, B., Chazin, W.J.

Assembly

calmodulin IQ motif complex

Entity

1. calmodulin (polymer, Thiol state: all free), 148 monomers, 16706.21 Da Detail

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

2. IQ motif (polymer, Thiol state: not present), 31 monomers, 3522.048 Da Detail

GPGSEEVSAM VIQRAFRRHL LQRSLKHASF L

Total weight

20228.26 Da

Max. entity weight

16706.21 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.4 %, Completeness: 94.2 %, Completeness (bb): 97.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.2 % (1920 of 2039)	97.1 % (1030 of 1061)	89.5 % (705 of 788)	97.4 % (185 of 190)
Backbone	97.7 % (1043 of 1068)	97.3 % (358 of 368)	97.7 % (512 of 524)	98.3 % (173 of 176)
Sidechain	91.6 % (1041 of 1137)	97.0 % (672 of 693)	83.0 % (357 of 430)	85.7 % (12 of 14)
Aromatic	44.5 % (57 of 128)	89.1 % (57 of 64)	0.0 % (0 of 64)
Methyl	98.3 % (173 of 176)	98.9 % (87 of 88)	97.7 % (86 of 88)

1. calmodulin

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

2. IQ motif

GPGSEEVSAM VIQRAFRRHL LQRSLKHASF L

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	calmodulin	natural abundance		1 mM
7	IQ_motif	natural abundance		1 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %
10	KCl	natural abundance		100 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2L53, Strand ID: A, B Detail

Release date

2010-12-21

Citation

Solution NMR structure of Apo-calmodulin in complex with the IQ motif of human cardiac sodium channel NaV1.5
Chagot, B., Chazin, W.J.
J. Mol. Biol. (2011), 406, 106-119, PubMed 21167176 , DOI 10.1016/j.jmb.2010.11.046 , Abstract

Related entities 1. calmodulin, : 11 : 88 entities Detail

Related entities 2. IQ motif, : 1 : 7 : 65 entities Detail

Interaction partners 2. IQ motif, : 13 interactors Detail

More details for 13 interactors identified by 9 citations

Experiments performed 12 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker DRX - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	calmodulin	natural abundance		1 mM
7	IQ_motif	natural abundance		1 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %
10	KCl	natural abundance		100 mM

2 2D 1H-1H COSY

Instrument

Bruker DRX - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	calmodulin	natural abundance		1 mM
7	IQ_motif	natural abundance		1 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %
10	KCl	natural abundance		100 mM

3 2D 1H-15N HSQC

Instrument

Bruker DRX - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

4 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

5 3D HNCACB

Instrument

Bruker DRX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

6 3D 1H-15N NOESY

Instrument

Bruker DRX - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

7 3D 1H-13C NOESY

Instrument

Bruker DRX - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

8 3D HNCO

Instrument

Bruker DRX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

9 3D H(CCO)NH

Instrument

Bruker DRX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

10 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

11 2D 1H-1H TOCSY

Instrument

Bruker DRX - 800 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	calmodulin	natural abundance		1 mM
7	IQ_motif	natural abundance		1 mM
8	H2O	natural abundance		95 %
9	D2O	natural abundance		5 %
10	KCl	natural abundance		100 mM

12 3D HCCH-COSY

Instrument

Bruker DRX - 600 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	calmodulin	[U-99% 13C; U-99% 15N]		1 mM
2	IQ_motif	[U-99% 13C; U-99% 15N]		1 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %
5	KCl	natural abundance		100 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17264_2l53.nef
Input source #2: Coordindates	2l53.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-------100
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI

-------110-------120-------130-------140--------
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
||||||||||||||||||||||||||||||||||||||||||||||||
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

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

----------1910------1920-------
GPGSEEVSAMVIQRAFRRHLLQRSLKHASFL
|||||||||||||||||||||||||||||||
GPGSEEVSAMVIQRAFRRHLLQRSLKHASFL
--------10--------20--------30-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0
B	B	31	0	0	100.0

Content subtype: combined_17264_2l53.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1946		99.3 (chain: A, length: 148), 100.0 (chain: B, length: 31)
1	Distance restraints	AMBER_distance_constraints_2	OK	4839 (1)	noe	99.3 (chain: A, length: 148), 100.0 (chain: B, length: 31)
1	Dihedral angle restraints	AMBER_dihedral_3	OK	246 (246)	.	87.2 (chain: A, length: 148), 67.7 (chain: B, length: 31)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 99.3%
  - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 1040
  - ¹³C chemical shifts: 713
  - ¹⁵N chemical shifts: 193
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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

Distance restraints

Saveframe: AMBER_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 99.3%
  - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 100.0%
- Total number of restraints: 4734
- Weight of restraints: 1.0 (4734)
- Potential type of restraints: square-well-parabolic (4734)
- Range of distance target values: 2.58, 5.82 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 87.2%
  - Entity_assembly_ID: B, Chain length: 31, Sequence coverage: 67.7%
- Total number of restraints: 246
- Total number of restraints per polymer type: 246
- Weight of restraints: 1.0 (246)
- Potential type of restraints: square-well-parabolic (246)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords calmodulin, complex, IQ motif