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Found 1 Document (0.623 seconds)

BMRB: 30379

6BV7

NMR structure of Sodium/Calcium Exchanger 1 (NCX1) Two-helix Bundle (THB) domain

Authors

Yuan, J., Yuan, C., Bruschweiler, R.

Assembly

Sodium/calcium exchanger 1

Entity

1. Sodium/calcium exchanger 1 (polymer, Thiol state: not present), 57 monomers, 6777.454 Da Detail

SNAVLEVDER DQDDEEARRE MARILKELKQ KHPEKEIEQL IELANYQVLS QQQKSRA

Formula weight

6777.454 Da

Source organism

Canis lupus familiaris

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.5 %, Completeness: 89.0 %, Completeness (bb): 93.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.0 % (617 of 693)	83.6 % (311 of 372)	95.3 % (244 of 256)	95.4 % (62 of 65)
Backbone	93.8 % (319 of 340)	92.9 % (105 of 113)	93.6 % (160 of 171)	96.4 % (54 of 56)
Sidechain	85.9 % (352 of 410)	79.5 % (206 of 259)	97.2 % (138 of 142)	88.9 % (8 of 9)
Aromatic	100.0 % (12 of 12)	100.0 % (6 of 6)	100.0 % (6 of 6)
Methyl	87.9 % (51 of 58)	82.8 % (24 of 29)	93.1 % (27 of 29)

1. entity 1

SNAVLEVDER DQDDEEARRE MARILKELKQ KHPEKEIEQL IELANYQVLS QQQKSRA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM [U-15N] NCX1_THB, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NCX1_THB	[U-15N]	300 uM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM [U-13C; U-15N] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM [U-13C; U-15N] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 mM
8	sodium phosphate	natural abundance	20 mM
9	NCX1 THB	[U-13C; U-15N]	300 uM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	NCX1 THB	natural abundance	300 uM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM [U-10% 13C] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
13	sodium chloride	natural abundance	100 mM
14	sodium phosphate	natural abundance	20 mM
15	NCX1 THB	[U-10% 13C]	300 uM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	0.0 ppm	external	direct	0.2514495
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	0.0 ppm	external	direct	0.2514495
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	0.0 ppm	external	direct	0.2514495
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	0.0 ppm	external	direct	0.2514495
¹H	DSS	methyl protons	0.0 ppm	external	direct	1.0

Referencing offset: 0.24 ppm, Outliers: 1 Detail

Release date

2018-01-01

Citation

The Intracellular Loop of the Na+/Ca2+ Exchanger Contains an "Awareness Ribbon" Shaped Two-helix Bundle Domain
Yuan, J., Yuan, C., Xie, M., Yu, L., Bruschweiler-Li, L., Bruschweiler, R.
Biochemistry (2018), 57, 5096-5104, PubMed 29898361 , DOI 10.1021/acs.biochem.8b00300 , Abstract

Related entities 1. Sodium/calcium exchanger 1, : 1 : 6 : 15 entities Detail

Interaction partners 1. Sodium/calcium exchanger 1, : 17 interactors Detail

More details for 17 interactors identified by 3 citations

Experiments performed 21 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM [U-15N] NCX1_THB, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NCX1_THB	[U-15N]	300 uM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM [U-13C; U-15N] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 mM
8	sodium phosphate	natural abundance	20 mM
9	NCX1 THB	[U-13C; U-15N]	300 uM

3 3D HNCA

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM [U-13C; U-15N] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

4 3D HN(CO)CA

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

5 3D HNCO

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

6 3D HNCACO

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

7 3D HNCACB

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

8 3D HN(COCA)CB

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

9 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 mM
8	sodium phosphate	natural abundance	20 mM
9	NCX1 THB	[U-13C; U-15N]	300 uM

10 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 mM
8	sodium phosphate	natural abundance	20 mM
9	NCX1 THB	[U-13C; U-15N]	300 uM

11 3D H(CO)NH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

12 3D (H)CC(CO)NH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

13 2D aromatic TROSY-HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 mM
8	sodium phosphate	natural abundance	20 mM
9	NCX1 THB	[U-13C; U-15N]	300 uM

14 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	NCX1 THB	natural abundance	300 uM

15 3D HNHB

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NCX1_THB	[U-15N]	300 uM
2	sodium chloride	natural abundance	100 mM
3	sodium phosphate	natural abundance	20 mM

16 2D DQF-COSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	20 mM
12	NCX1 THB	natural abundance	300 uM

17 2D 10%-13C CT-HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 300 uM [U-10% 13C] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O

#	Name	Isotope labeling	Concentration
13	sodium chloride	natural abundance	100 mM
14	sodium phosphate	natural abundance	20 mM
15	NCX1 THB	[U-10% 13C]	300 uM

18 3D 15N-edited NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

19 3D 15N-edited CNH-NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
4	sodium chloride	natural abundance	100 mM
5	sodium phosphate	natural abundance	20 mM
6	NCX1 THB	[U-13C; U-15N]	300 uM

20 3D 13C-edited NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 mM
8	sodium phosphate	natural abundance	20 mM
9	NCX1 THB	[U-13C; U-15N]	300 uM

21 3D 13C-edited CCH-NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	100 mM
8	sodium phosphate	natural abundance	20 mM
9	NCX1 THB	[U-13C; U-15N]	300 uM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30379_6bv7.nef
Input source #2: Coordindates	6bv7.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

-------280-------290-------300-------310-------320-------
SNAVLEVDERDQDDEEARREMARILKELKQKHPEKEIEQLIELANYQVLSQQQKSRA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SNAVLEVDERDQDDEEARREMARILKELKQKHPEKEIEQLIELANYQVLSQQQKSRA
--------10--------20--------30--------40--------50-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	57	0	0	100.0

Content subtype: combined_30379_6bv7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	640		96.5 (chain: A, length: 57)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	685 (1)	noe	94.7 (chain: A, length: 57)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	56 (1)	hbond	63.2 (chain: A, length: 57)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	74 (74)	.	66.7 (chain: A, length: 57)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 96.5%
- Total number of assignments
  - ¹H chemical shifts: 320
  - ¹³C chemical shifts: 258
  - ¹⁵N chemical shifts: 62
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
282	GLN	CD	180.283
300	GLN	CD	180.283
309	GLN	CD	180.076
315	ASN	CG	175.633
317	GLN	CD	179.207
321	GLN	CD	180.392
322	GLN	CD	180.296
323	GLN	CD	180.411

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	372	320	86.0
¹³C chemical shifts	256	250	97.7
¹⁵N chemical shifts	70	62	88.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	113	109	96.5
¹³C chemical shifts	114	110	96.5
¹⁵N chemical shifts	56	54	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	259	211	81.5
¹³C chemical shifts	142	140	98.6
¹⁵N chemical shifts	14	8	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	30	100.0
¹³C chemical shifts	30	30	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	6	6	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 94.7%
- Total number of restraints: 685
- Weight of restraints: 1.0 (685)
- Potential type of restraints: square-well-parabolic (685)
- Range of distance target values: 2.35, 5.4 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 63.2%
  - Total number of restraints: 56
  - Weight of restraints: 1.0 (56)
  - Potential type of restraints: square-well-parabolic (56)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: A, Chain length: 57, Sequence coverage: 66.7%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MEMBRANE PROTEIN, Two-helix Bundle

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Found 1 Document (0.623 seconds)

BMRB: 30379

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Sodium/calcium exchanger 1, : 1 : 6 : 15 entities Detail

Interaction partners 1. Sodium/calcium exchanger 1, : 17 interactors Detail

Experiments performed 21 experiments Detail

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NMR combined restraints 5 contents Detail