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BMRB: 25592

2N29

Solution-state NMR structure of Vpu cytoplasmic domain

Authors

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

Assembly

Vpu cytoplasmic domain

Entity

1. HIV-1 Virus protein U (polymer, Thiol state: not present), 54 monomers, 6255.875 Da Detail

EYRKILRQRK IDRLIDRLIE RAEDSGNESE GEISALVELG VELGHHAPWD VDDL

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

Total weight

6416.999 Da

Max. entity weight

6255.875 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 47.7 %, Completeness (bb): 92.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	47.7 % (299 of 627)	31.9 % (105 of 329)	58.7 % (142 of 242)	92.9 % (52 of 56)
Backbone	92.9 % (299 of 322)	94.6 % (105 of 111)	89.9 % (142 of 158)	98.1 % (52 of 53)
Sidechain	12.1 % (43 of 355)	0.0 % (0 of 218)	32.1 % (43 of 134)	0.0 % (0 of 3)
Aromatic	0.0 % (0 of 28)	0.0 % (0 of 14)	0.0 % (0 of 13)	0.0 % (0 of 1)
Methyl	3.0 % (2 of 66)	0.0 % (0 of 33)	6.1 % (2 of 33)

1. HIV-1 Virus protein U

EYRKILRQRK IDRLIDRLIE RAEDSGNESE GEISALVELG VELGHHAPWD VDDL

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
5	Vpu Cytoplasmic domain	[U-100% 13C; U-100% 15N]		0.5 mM
6	DHPC	natural abundance		100 mM
7	H20	natural abundance		90 %
8	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 1 models in PDB: 2N29, 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 : 1 : 4 : 30 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 3D_15N-separated_NOESY

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

2 2D_15N/1N_HSQC

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

3 2D_15N/1N_HSQCIPAP

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D_HNCA

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D_HCCCONH

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D_CCCONH

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D_15N/13C'/13C

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D_HNCO

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D_HNCACB

Instrument

Bruker AVANCE - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0, Details 100mM DHPC; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Vpu Cytoplasmic domain	[U-100% 15N]		0.5 mM
2	DHPC	natural abundance		100 mM
3	H20	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25592_2n29.nef
Input source #2: Coordindates	2n29.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----
EYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVELGVELGHHAPWDVDDL
||||||||||||||||||||||||||||||||||||||||||||||||||||||
EYRKILRQRKIDRLIDRLIERAEDSGNESEGEISALVELGVELGHHAPWDVDDL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	54	0	0	100.0

Content subtype: combined_25592_2n29.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	298		100.0 (chain: A, length: 54)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	901 (1)	noe	100.0 (chain: A, length: 54)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	62 (62)	.	68.5 (chain: A, length: 54)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	39 (39)	.	72.2 (chain: A, length: 54)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 104
  - ¹³C chemical shifts: 142
  - ¹⁵N chemical shifts: 52
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 100.0%
- Total number of restraints: 898
- Weight of restraints: 1.0 (898)
- Potential type of restraints: square-well-parabolic (898)
- Range of distance target values: 2.5, 5.0 (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: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 68.5%
- Total number of restraints: 62
- Total number of restraints per polymer type: 62
- Weight of restraints: 1.0 (62)
- Potential type of restraints: square-well-parabolic (62)
- 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: 54, Sequence coverage: 72.2%
- Total number of restraints: 39
- Potential type of restraints: undefined (39)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords alpha helix