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BMRB: 25591

2N28

Solid-state NMR structure of Vpu

Authors

Zhang, H., Lin, E.C., Tian, Y., Das, B.B., Opella, S.J.

Assembly

Vpu from HIV-1

Entity

1. HIV-1 Virus protein U (polymer, Thiol state: not present), 81 monomers, 9137.560 Da Detail

MQPIQIAIVA LVVAIIIAIV VWSIVIIEYR KILRQRKIDR LIDRLIERAE DSGNESEGEI SALVELGVEL GHHAPWDVDD L

2. 4-(trifluoromethyl)aniline (non-polymer), 161.124 Da

Total weight

9298.684 Da

Max. entity weight

9137.56 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 70.4 %, Completeness: 35.3 %, Completeness (bb): 47.8 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	35.3 % (164 of 464)	30.6 % (116 of 379)	56.5 % (48 of 85)
Backbone	47.8 % (152 of 318)	43.5 % (104 of 239)	60.8 % (48 of 79)
Sidechain	9.4 % (21 of 223)	9.7 % (21 of 217)	0.0 % (0 of 6)
Aromatic	15.0 % (3 of 20)	16.7 % (3 of 18)	0.0 % (0 of 2)
Methyl	5.6 % (4 of 71)	5.6 % (4 of 71)

1. HIV-1 Virus protein U

MQPIQIAIVA LVVAIIIAIV VWSIVIIEYR KILRQRKIDR LIDRLIERAE DSGNESEGEI SALVELGVEL GHHAPWDVDD L

Show sample condition

Sample

Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

Protein Blocks Logo

Calculated from 1 models in PDB: 2N28, Strand ID: A Detail

Release date

2015-09-27

Citation

Structural determination of virus protein U from HIV-1 by NMR in membrane environments
Zhang, H., Lin, E.C., Tian, Y., Das, B.B., Opella, S.J.
Biochim. Biophys. Acta (2015), 1848, 3007-3018, PubMed 26362058 , DOI 10.1016/j.bbamem.2015.09.008 , Abstract

Related entities 1. HIV-1 Virus protein U, : 1 : 22 entities Detail

Interaction partners 1. HIV-1 Virus protein U, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 9 experiments Detail

1 2D_13C/13C_PDSD

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

2 2D_13C/15N_HETCOR

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

3 2D_13C/13C_TOBSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

4 2D_13C-1H_DC/13C_SLF

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

5 2D_15N-1H_DC/13C_SLF

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

6 3D_15N/13CA/13C

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

7 3D_15N/13C'/13C

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

8 3D_1H-15N_DC/15N/13CA_SLF

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

9 3D_1H-13C_DC/15N/13CA_SLF

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100%H2O, Pressure 1 atm, Temperature 298 K, pH 7.3, Details DMPC proteoliposomes

#	Name	Isotope labeling	Type	Concentration
1	HIV-1 Virus protein U	[U-100% 13C; U-100% 15N]		8.5 mM
2	H20	natural abundance		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints, RDC restraints	combined_25591_2n28.nef
Input source #2: Coordindates	2n28.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-
MQPIQIAIVALVVAIIIAIVVWSIVIIEYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVELGVELGHHAPWDVDDL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQPIQIAIVALVVAIIIAIVVWSIVIIEYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVELGVELGHHAPWDVDDL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	81	0	0	100.0

Content subtype: combined_25591_2n28.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	159		65.4 (chain: A, length: 81)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	90 (90)	.	63.0 (chain: A, length: 81)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	57 (57)	.	51.9 (chain: A, length: 81)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 65.4%
- Total number of assignments
  - ¹³C chemical shifts: 112
  - ¹⁵N chemical shifts: 47
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 63.0%
- Total number of restraints: 90
- Total number of restraints per polymer type: 90
- Weight of restraints: 1.0 (90)
- Potential type of restraints: square-well-parabolic (90)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 51.9%
- Total number of restraints: 57
- Potential type of restraints: square-well-parabolic (1), undefined (56)
- Range of observed RDC values: -7.39, -7.39 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords alpha helix