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BMRB: 30065

5JDP

E73V mutant of the human voltage-dependent anion channel

Authors

Jaremko, M., Jaremko, L., Villinger, S., Schmidt, C., Giller, K., Griesinger, C., Becker, S., Zweckstetter, M.

Assembly

Voltage-dependent anion-selective channel protein 1

Entity

1. Voltage-dependent anion-selective channel protein 1 (polymer), 285 monomers, 30941.36 Da Detail

SAVPPTYADL GKSARDVFTK GYGFGLIKLD LKTKSENGLE FTSSGSANTE TTKVTGSLET KYRWTEYGLT FTVKWNTDNT LGTEITVEDQ LARGLKLTFD SSFSPNTGKK NAKIKTGYKR EHINLGCDMD FDIAGPSIRG ALVLGYEGWL AGYQMNFETA KSRVTQSNFA VGYKTDEFQL HTNVNDGTEF GGSIYQKVNK KLETAVNLAW TAGNSNTRFG IAAKYQIDPD ACFSAKVNNS SLIGLGYTQT LKPGIKLTLS ALLDGKNVNA GGHKLGLGLE FQARS

Formula weight

30941.36 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 36.5 %, Completeness (bb): 62.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	36.5 % (1187 of 3248)	22.8 % (381 of 1673)	43.2 % (546 of 1265)	83.9 % (260 of 310)
Backbone	62.5 % (1061 of 1698)	48.0 % (286 of 596)	63.2 % (520 of 823)	91.4 % (255 of 279)
Sidechain	9.4 % (170 of 1803)	8.9 % (96 of 1077)	9.9 % (69 of 695)	16.1 % (5 of 31)
Aromatic	3.8 % (11 of 288)	4.9 % (7 of 144)	0.0 % (0 of 140)	100.0 % (4 of 4)
Methyl	13.5 % (42 of 310)	14.8 % (23 of 155)	12.3 % (19 of 155)

1. Voltage-dependent anion-selective channel protein 1

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.8, Details 0.8 mM U- 2H, 15N_sample E73V mutant of the Voltage-dependent anion channel 1, 2 % U- 2H LDAO, 20 mM U- 2H TRIS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	E73V mutant of the Voltage-dependent anion channel 1	[U-2H; U-15N]	0.8 mM
2	LDAO	[U-2H]	2 %
3	TRIS	[U-2H]	20 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5JDP, Strand ID: A Detail

Heteronucl. T₁

534 T₁ values in 3 lists
Coherence Iz, Field strength (¹H) 600 MHz, 900 MHz, Pressure 1 atm, Temperature 310 K, pH 6.8 Detail

Heteronucl. T₂

534 T₂ values in 3 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, 700 MHz, 900 MHz, Pressure 1 atm, Temperature 310 K, pH 6.8 Detail

Heteronucl. T₁/T₂

356 T₁/T₂ values in 2 lists
Field strength (¹H) 600 MHz, 900 MHz, Pressure 1 atm, Temperature 310 K, pH 6.8 Detail

Release date

2016-08-07

Citation

High-Resolution NMR Determination of the Dynamic Structure of Membrane Proteins
Jaremko, M., Jaremko, L., Villinger, S., Schmidt, C., Giller, K., Griesinger, C., Becker, S., Zweckstetter, M.
Angew. Chem Int Ed Engl. (2016), 55, 10518-10521, PubMed 27461260 , DOI 10.1002/anie.201602639 , Abstract

Related entities 1. Voltage-dependent anion-selective channel protein 1, : 1 : 12 : 103 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 7 experiments Detail

1 R1 relaxation rate

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.8, Details 0.8 mM U- 2H, 15N_sample E73V mutant of the Voltage-dependent anion channel 1, 2 % U- 2H LDAO, 20 mM U- 2H TRIS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	E73V mutant of the Voltage-dependent anion channel 1	[U-2H; U-15N]	0.8 mM
2	LDAO	[U-2H]	2 %
3	TRIS	[U-2H]	20 mM

2 R2 relaxation rate

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	E73V mutant of the Voltage-dependent anion channel 1	[U-2H; U-15N]	0.8 mM
2	LDAO	[U-2H]	2 %
3	TRIS	[U-2H]	20 mM

3 R1 relaxation rate

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	E73V mutant of the Voltage-dependent anion channel 1	[U-2H; U-15N]	0.8 mM
2	LDAO	[U-2H]	2 %
3	TRIS	[U-2H]	20 mM

4 R2 relaxation rate

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	E73V mutant of the Voltage-dependent anion channel 1	[U-2H; U-15N]	0.8 mM
2	LDAO	[U-2H]	2 %
3	TRIS	[U-2H]	20 mM

5 R1 relaxation rate

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	E73V mutant of the Voltage-dependent anion channel 1	[U-2H; U-15N]	0.8 mM
2	LDAO	[U-2H]	2 %
3	TRIS	[U-2H]	20 mM

6 R2 relaxation rate

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	E73V mutant of the Voltage-dependent anion channel 1	[U-2H; U-15N]	0.8 mM
2	LDAO	[U-2H]	2 %
3	TRIS	[U-2H]	20 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	E73V mutant of the Voltage-dependent anion channel 1	[U-2H; U-15N]	0.8 mM
2	LDAO	[U-2H]	2 %
3	TRIS	[U-2H]	20 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30065_5jdp.nef
Input source #2: Coordindates	5jdp.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
SAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTVKWNTDNTLGTEITVEDQLARGLKLTFD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTVKWNTDNTLGTEITVEDQLARGLKLTFD

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
SSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNK

-------210-------220-------230-------240-------250-------260-------270-------280-----
KLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQARS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQARS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	285	0	0	100.0

Content subtype: combined_30065_5jdp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	971		93.0 (chain: A, length: 285)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	675 (1)	noe	87.7 (chain: A, length: 285)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	256 (1)	hbond	67.0 (chain: A, length: 285)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	452 (452)	.	84.9 (chain: A, length: 285)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 285, Sequence coverage: 93.0%
- Total number of assignments
  - ¹³C chemical shifts: 466
  - ¹H chemical shifts: 253
  - ¹⁵N chemical shifts: 252
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1265	466	36.8
¹H chemical shifts	1673	253	15.1
¹⁵N chemical shifts	318	252	79.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	570	466	81.8
¹H chemical shifts	596	248	41.6
¹⁵N chemical shifts	279	248	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	695	0	0.0
¹H chemical shifts	1077	5	0.5
¹⁵N chemical shifts	39	4	10.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	157	0	0.0
¹H chemical shifts	157	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	140	0	0.0
¹H chemical shifts	144	5	3.5
¹⁵N chemical shifts	4	4	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 285, Sequence coverage: 87.7%
- Total number of restraints: 675
- Weight of restraints: 1.0 (675)
- Potential type of restraints: square-well-parabolic (675)
- Range of distance target values: 3.1, 4.5 (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: 285, Sequence coverage: 67.0%
  - Total number of restraints: 256
  - Weight of restraints: 1.0 (256)
  - Potential type of restraints: square-well-parabolic (256)
  - 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: 285, Sequence coverage: 84.9%
- Total number of restraints: 452
- Total number of restraints per polymer type: 452
- Weight of restraints: 1.0 (452)
- Potential type of restraints: square-well-parabolic (452)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Membrane Protein, Protein dynamics, Relaxation, Sparse data, Structure refinement

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Found 1 Document (3.934 seconds)

BMRB: 30065

Sample

Related entities 1. Voltage-dependent anion-selective channel protein 1, : 1 : 12 : 103 entities Detail

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

Experiments performed 7 experiments Detail

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NMR combined restraints 5 contents Detail