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Found 1 Document (3.137 seconds)

BMRB: 34457

6TIR

Refined solution NMR structure of hVDAC-1 in detergent micelles

Authors

Boehm, R., Hiller, S., Wagner, G.

Assembly

Voltage-dependent anion-selective channel protein 1

Entity

1. Voltage-dependent anion-selective channel protein 1 (polymer, Thiol state: all free), 291 monomers, 31837.31 Da Detail

MAVPPTYADL GKSARDVFTK GYGFGLIKLD LKTKSENGLE FTSSGSANTE TTKVTGSLET KYRWTEYGLT FTEKWNTDNT LGTEITVEDQ LARGLKLTFD SSFSPNTGKK NAKIKTGYKR EHINLGCDMD FDIAGPSIRG ALVLGYEGWL AGYQMNFETA KSRVTQSNFA VGYKTDEFQL HTNVNDGTEF GGSIYQKVNK KLETAVNLAW TAGNSNTRFG IAAKYQIDPD ACFSAKVNNS SLIGLGYTQT LKPGIKLTLS ALLDGKNVNA GGHKLGLGLE FQALEHHHHH H

Formula weight

31837.31 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.3 %, Completeness: 45.0 %, Completeness (bb): 69.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	45.0 % (1497 of 3327)	26.7 % (457 of 1713)	60.2 % (781 of 1298)	82.0 % (259 of 316)
Backbone	69.8 % (1210 of 1734)	47.9 % (291 of 608)	79.2 % (666 of 841)	88.8 % (253 of 285)
Sidechain	27.1 % (502 of 1852)	15.1 % (167 of 1105)	45.9 % (329 of 716)	19.4 % (6 of 31)
Aromatic	7.4 % (23 of 312)	7.7 % (12 of 156)	4.6 % (7 of 152)	100.0 % (4 of 4)
Methyl	63.5 % (197 of 310)	57.4 % (89 of 155)	69.7 % (108 of 155)

1. entity 1

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM U-99%-2H,13C,15N hVDAC-1, 3 % no LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	hVDAC-1	[U-99%-2H; U-13C; U-15N]		0.6 mM
2	LDAO	no		3 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM [ U -99%- 2 H, 13 C, 15 N; 99%- 1 H delta -IL; 99%- 1 H gamma -V] hVDAC-1, 3 % [U-99% 2H] LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	hVDAC-1	[U-99%-2H, 13C, 15N; 99%-1H delta-IL; 99%-1H gamma-V]		0.6 mM
4	LDAO	[U-99% 2H]		3 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM [ U -99%- 2 H, 15 N; 99%- 1 H delta , 13 C delta -IL; 99%- 1 H gamma , 13 C gamma -V] hVDAC-1, 3 % [U-99% 2H] LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
5	hVDAC-1	[U-99%-2H, 15N; 99%-1H delta, 13C delta-IL; 99%-1H gamma, 13C gamma-V]		0.6 mM
6	LDAO	[U-99% 2H]		3 %

LACS Plot; CA

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

Referencing offset: 0.49 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.49 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.96 ppm, Outliers: 3 Detail

Release date

2019-11-26

Citation

The Structural Basis for Low Conductance in the Membrane Protein VDAC upon β-NADH Binding and Voltage Gating
Boehm, R., Hiller, S., Amodeo, G.F., Murlidaran, S., Chavali, S., Wagner, G., Brannigan, G., Winterhalter, M.
Structure (2020), 28, 206-214, PubMed 31862297 , DOI 10.1016/j.str.2019.11.015 , Abstract

Related entities 1. Voltage-dependent anion-selective channel protein 1, : 1 : 4 : 8 : 101 entities Detail

Interaction partners 1. Voltage-dependent anion-selective channel protein 1, : 95 interactors Detail

More details for 95 interactors identified by 35 citations

Experiments performed 8 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM [ U -99%- 2 H, 13 C, 15 N; 99%- 1 H delta -IL; 99%- 1 H gamma -V] hVDAC-1, 3 % [U-99% 2H] LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	hVDAC-1	[U-99%-2H, 13C, 15N; 99%-1H delta-IL; 99%-1H gamma-V]		0.6 mM
4	LDAO	[U-99% 2H]		3 %

2 3D 1H-13C NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM [ U -99%- 2 H, 15 N; 99%- 1 H delta , 13 C delta -IL; 99%- 1 H gamma , 13 C gamma -V] hVDAC-1, 3 % [U-99% 2H] LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
5	hVDAC-1	[U-99%-2H, 15N; 99%-1H delta, 13C delta-IL; 99%-1H gamma, 13C gamma-V]		0.6 mM
6	LDAO	[U-99% 2H]		3 %

3 4D NUS-MDD-1H-13C-13C

Instrument

Bruker AVANCE - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	hVDAC-1	[U-99%-2H, 13C, 15N; 99%-1H delta-IL; 99%-1H gamma-V]		0.6 mM
4	LDAO	[U-99% 2H]		3 %

4 4D NUS-MDD-1H-15N-13C

Instrument

Bruker AVANCE - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	hVDAC-1	[U-99%-2H, 15N; 99%-1H delta, 13C delta-IL; 99%-1H gamma, 13C gamma-V]		0.6 mM
6	LDAO	[U-99% 2H]		3 %

5 3D HNCO

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM U-99%-2H,13C,15N hVDAC-1, 3 % no LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	hVDAC-1	[U-99%-2H; U-13C; U-15N]		0.6 mM
2	LDAO	no		3 %

6 3D HNCA

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM U-99%-2H,13C,15N hVDAC-1, 3 % no LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	hVDAC-1	[U-99%-2H; U-13C; U-15N]		0.6 mM
2	LDAO	no		3 %

7 3D HNCACB

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM U-99%-2H,13C,15N hVDAC-1, 3 % no LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	hVDAC-1	[U-99%-2H; U-13C; U-15N]		0.6 mM
2	LDAO	no		3 %

8 3D HN(CO)CA

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 6.5, Details 0.6 mM U-99%-2H,13C,15N hVDAC-1, 3 % no LDAO, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	hVDAC-1	[U-99%-2H; U-13C; U-15N]		0.6 mM
2	LDAO	no		3 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34457_3.str
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

Content subtype: bmr34457_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1504		87.3 (chain: 1, length: 291)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 291, Sequence coverage: 87.3%
- Total number of assignments
  - ¹H chemical shifts: 510
  - ¹³C chemical shifts: 739
  - ¹⁵N chemical shifts: 255
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
111	ASN	CG	176.475
116	THR	HG1	4.253
127	CYS	HG	1.154
196	GLN	CD	176.396

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1713	338	19.7
¹³C chemical shifts	1298	737	56.8
¹⁵N chemical shifts	323	255	78.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	608	249	41.0
¹³C chemical shifts	582	434	74.6
¹⁵N chemical shifts	285	249	87.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1105	89	8.1
¹³C chemical shifts	716	303	42.3
¹⁵N chemical shifts	38	6	15.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	158	85	53.8
¹³C chemical shifts	158	104	65.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	156	4	2.6
¹³C chemical shifts	152	0	0.0
¹⁵N chemical shifts	4	4	100.0

Keywords TRANSPORT PROTEIN, beta-barrel membrane protein VDAC pore

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Found 1 Document (3.137 seconds)

BMRB: 34457

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Voltage-dependent anion-selective channel protein 1, : 1 : 4 : 8 : 101 entities Detail

Interaction partners 1. Voltage-dependent anion-selective channel protein 1, : 95 interactors Detail

Experiments performed 8 experiments Detail

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Chemical shift validation 3 contents Detail