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Found 1 Document (0.532 seconds)

BMRB: 34309

6HH0

Yeast V-ATPase transmembrane helix 7 NMR structure in DPC micelles

Authors

Zangger, K., Hohlweg, W., Wagner, G.

Assembly

V-type proton ATPase subunit a, vacuolar isoform

Entity

1. V-type proton ATPase subunit a, vacuolar isoform (polymer, Thiol state: not present), 25 monomers, 2825.270 Da Detail

KKSHTASYLR LWALSLAHAQ LSSKK

Formula weight

2825.27 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 47.0 %, Completeness (bb): 41.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	47.0 % (143 of 304)	78.5 % (124 of 158)	12.6 % (15 of 119)	14.8 % (4 of 27)
Backbone	41.3 % (62 of 150)	96.0 % (48 of 50)	13.3 % (10 of 75)	16.0 % (4 of 25)
Sidechain	47.5 % (85 of 179)	70.4 % (76 of 108)	13.0 % (9 of 69)	0.0 % (0 of 2)
Aromatic	46.4 % (13 of 28)	92.9 % (13 of 14)	0.0 % (0 of 13)	0.0 % (0 of 1)
Methyl	60.0 % (18 of 30)	100.0 % (15 of 15)	20.0 % (3 of 15)

1. entity 1

KKSHTASYLR LWALSLAHAQ LSSKK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 100 mM [U-99% 2H] Deuterated DPC, 50 mM potassium phosphate, 0.02 % sodium azide, 1 mM 13C and 15N labeled aminoacids 8 and 12 TM7 peptide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Deuterated DPC	[U-99% 2H]	100 mM
2	potassium phosphate	none	50 mM
3	sodium azide	none	0.02 %
4	TM7 peptide	13C and 15N labeled aminoacids 8 and 12	1 mM

Release date

2018-09-03

Citation

A cation-π interaction in a transmembrane helix of vacuolar ATPase retains the proton-transporting arginine in a hydrophobic environment
Hohlweg, W., Wagner-Lichtenegger, G., Hofbauer, H., Sarkleti, F., Setz, M., Gubensak, N., Lichtenegger, S., Falsone, F., Wolinski, H., Kosol, S., Oostenrbink, C., Kohlwein, S., Zangger, K.
J. Biol. Chem. (2018), 293, 18977-18988, PubMed 30209131 , DOI 10.1074/jbc.RA118.005276 , Abstract

Related entities 1. V-type proton ATPase subunit a, vacuolar isoform, : 1 : 2 : 13 : 75 entities Detail

Interaction partners 1. V-type proton ATPase subunit a, vacuolar isoform, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 5 experiments Detail

1 2D NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 100 mM [U-99% 2H] Deuterated DPC, 50 mM potassium phosphate, 0.02 % sodium azide, 1 mM 13C and 15N labeled aminoacids 8 and 12 TM7 peptide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Deuterated DPC	[U-99% 2H]	100 mM
2	potassium phosphate	none	50 mM
3	sodium azide	none	0.02 %
4	TM7 peptide	13C and 15N labeled aminoacids 8 and 12	1 mM

2 2D TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Deuterated DPC	[U-99% 2H]	100 mM
2	potassium phosphate	none	50 mM
3	sodium azide	none	0.02 %
4	TM7 peptide	13C and 15N labeled aminoacids 8 and 12	1 mM

3 3D NOESY-N-HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Deuterated DPC	[U-99% 2H]	100 mM
2	potassium phosphate	none	50 mM
3	sodium azide	none	0.02 %
4	TM7 peptide	13C and 15N labeled aminoacids 8 and 12	1 mM

4 2D HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Deuterated DPC	[U-99% 2H]	100 mM
2	potassium phosphate	none	50 mM
3	sodium azide	none	0.02 %
4	TM7 peptide	13C and 15N labeled aminoacids 8 and 12	1 mM

5 3D NOESY C-HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Deuterated DPC	[U-99% 2H]	100 mM
2	potassium phosphate	none	50 mM
3	sodium azide	none	0.02 %
4	TM7 peptide	13C and 15N labeled aminoacids 8 and 12	1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34309_6hh0.nef
Input source #2: Coordindates	6hh0.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-----
KKSHTASYLRLWALSLAHAQLSSKK
|||||||||||||||||||||||||
KKSHTASYLRLWALSLAHAQLSSKK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	25	0	0	100.0

Content subtype: combined_34309_6hh0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	134		100.0 (chain: A, length: 25)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	817 (1)	noe	100.0 (chain: A, length: 25)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	18 (1)	hbond	88.0 (chain: A, length: 25)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	20 (20)	.	64.0 (chain: A, length: 25)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 128
  - ¹³C chemical shifts: 4
  - ¹⁵N chemical shifts: 2
- Completeness of assignments
  - Entity_assemble_ID: A
- 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)
2	LYS	HZ1	7.918
2	LYS	HZ2	7.918
2	LYS	HZ3	7.918
5	THR	HG1	1.219
10	ARG	HH11	7.0244

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	158	123	77.8
¹³C chemical shifts	119	4	3.4
¹⁵N chemical shifts	28	2	7.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	48	96.0
¹³C chemical shifts	50	1	2.0
¹⁵N chemical shifts	25	1	4.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	108	75	69.4
¹³C chemical shifts	69	3	4.3
¹⁵N chemical shifts	3	1	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	15	100.0
¹³C chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	13	92.9
¹³C chemical shifts	13	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 100.0%
- Total number of restraints: 723
- Weight of restraints: 1.0 (723)
- Potential type of restraints: square-well-parabolic (723)
- Range of distance target values: 2.29, 4.54 (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_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 88.0%
  - Total number of restraints: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: square-well-parabolic (18)
  - Range of distance target values: 2.8, 2.8 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 64.0%
- Total number of restraints: 20
- Total number of restraints per polymer type: 20
- Weight of restraints: 1.0 (20)
- Potential type of restraints: square-well-parabolic (20)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ATPasse, DPC micelle, NMR spectroscopy, membrane protein, transmembrane helix

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Found 1 Document (0.532 seconds)

BMRB: 34309

Sample

Related entities 1. V-type proton ATPase subunit a, vacuolar isoform, : 1 : 2 : 13 : 75 entities Detail

Interaction partners 1. V-type proton ATPase subunit a, vacuolar isoform, : 4 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail