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BMRB: 16381

2K4T

Sequence-specific resonance assignments of human VDAC-1 in LDAO micelles

Authors

Hiller, S., Garces, R.G., Malia, T.J., Orekhov, V.Y., Wagner, G.

Assembly

VDAC-1

Entity

1. VDAC-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

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 82.1 %, Completeness: 37.8 %, Completeness (bb): 56.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	37.8 % (1256 of 3327)	25.6 % (439 of 1713)	44.5 % (577 of 1298)	75.9 % (240 of 316)
Backbone	56.5 % (979 of 1734)	44.6 % (271 of 608)	56.2 % (473 of 841)	82.5 % (235 of 285)
Sidechain	26.0 % (481 of 1852)	15.2 % (168 of 1105)	43.0 % (308 of 716)	16.1 % (5 of 31)
Aromatic	7.1 % (22 of 312)	7.7 % (12 of 156)	3.9 % (6 of 152)	100.0 % (4 of 4)
Methyl	62.9 % (195 of 310)	58.1 % (90 of 155)	67.7 % (105 of 155)

1. VDAC-1

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 400 mM LDAO, 25 mM NaPi, 5 mM DTT, pH 7.0

#	Name	Isotope labeling	Concentration
1	VDAC-1	[U-13C; U-15N; U-2H]	1 mM
2	LDAO	natural abundance	400 mM
3	NaPi	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	H2O	natural abundance	93 %
6	D2O	natural abundance	7 %

LACS Plot; CA

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

Referencing offset: 0.87 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.87 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K4T, Strand ID: A Detail

Release date

2010-02-28

Citation

Structural and functional characterization of the integral membrane protein VDAC-1 in lipid bilayer nanodiscs
Raschle, T., Hiller, S., Yu, T., Rice, A.J., Walz, T., Wagner, G.
J. Am. Chem. Soc. (2009), 131, 17777-17779, PubMed 19916553 , DOI 10.1021/ja907918r , Abstract

Related entities 1. VDAC-1, : 1 : 4 : 8 : 101 entities Detail

Interaction partners 1. VDAC-1, : 95 interactors Detail

More details for 95 interactors identified by 35 citations

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16381_2k4t.nef
Input source #2: Coordindates	2k4t.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
MAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFD

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

-------210-------220-------230-------240-------250-------260-------270-------280-------290-
KLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQALEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KLETAVNLAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQALEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	291	0	0	100.0

Content subtype: combined_16381_2k4t.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1062		80.4 (chain: A, length: 291)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	785 (1)	noe	69.8 (chain: A, length: 291)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	556 (1)	hbond	49.5 (chain: A, length: 291)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	332 (332)	.	78.4 (chain: A, length: 291)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 291, Sequence coverage: 80.4%
- Total number of assignments
  - ¹³C chemical shifts: 513
  - ¹H chemical shifts: 316
  - ¹⁵N chemical shifts: 233
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
116	THR	HG1	4.363
182	THR	HG1	3.694

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1298	513	39.5
¹H chemical shifts	1713	314	18.3
¹⁵N chemical shifts	323	233	72.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	582	233	40.0
¹H chemical shifts	608	229	37.7
¹⁵N chemical shifts	285	229	80.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	716	280	39.1
¹H chemical shifts	1105	85	7.7
¹⁵N chemical shifts	38	4	10.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	158	99	62.7
¹H chemical shifts	158	81	51.3

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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 291, Sequence coverage: 69.8%
- Total number of restraints: 785
- Weight of restraints: 1.0 (785)
- Potential type of restraints: upper-bound-parabolic (785)
- Range of distance target values: 2.28, 5.7 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 291, Sequence coverage: 49.5%
  - Total number of restraints: 556
  - Weight of restraints: 1.0 (556)
  - Potential type of restraints: upper-bound-parabolic (556)
  - Range of distance target values: 1.8, 3.0 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 291, Sequence coverage: 78.4%
- Total number of restraints: 332
- Total number of restraints per polymer type: 332
- Weight of restraints: 1.0 (332)
- Potential type of restraints: square-well-parabolic (332)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MEMBRANE PROTEIN

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Found 1 Document (3.904 seconds)

BMRB: 16381

Sample

Chemical shift reference

Chemical shift reference

Related entities 1. VDAC-1, : 1 : 4 : 8 : 101 entities Detail

Interaction partners 1. VDAC-1, : 95 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail