BMRB Entry 25592

Name: Solution-state NMR structure of Vpu cytoplasmic domain
Published: 2015-09-28

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PDB ID: 2n29
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25592
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution-state NMR structure of Vpu cytoplasmic domain PubMed: 26362058

Deposition date: 2015-05-01 Original release date: 2015-09-28

Authors: Zhang, H.; Lin, E.; Tian, Y.; Das, B.; Opella, S.

Citation: Zhang, H.; Lin, E.; Tian, Y.; Das, B.; Opella, S.. "Structural determination of virus protein U from HIV-1 by NMR in membrane environments" Biochim. Biophys. Acta 1848, 3007-3018 (2015).

Assembly members:
HIV-1_Virus_protein_U, polymer, 54 residues, 6266.018 Da.
4-(trifluoromethyl)aniline, non-polymer, 161.124 Da.

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
HIV-1_Virus_protein_U: EYRKILRQRKIDRLIDRLIE RAEDSGNESEGEISALVELG VELGHHAPWDVDDL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	142
15N chemical shifts	52
1H chemical shifts	104

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HIV-1 Virus protein U	1
2	4-(TRIFLUOROMETHYL)ANILINE	2

Entities:

Entity 1, HIV-1 Virus protein U 54 residues - 6266.018 Da.

1

GLU

TYR

ARG

LYS

ILE

LEU

ARG

GLN

ARG

LYS

2

ILE

ASP

ARG

LEU

ILE

ASP

ARG

LEU

ILE

GLU

3

ARG

ALA

GLU

ASP

SER

GLY

ASN

GLU

SER

GLU

4

GLY

GLU

ILE

SER

ALA

LEU

VAL

GLU

LEU

GLY

5

VAL

GLU

LEU

GLY

HIS

ALA

PRO

TRP

ASP

6

VAL

ASP

LEU

Entity 2, 4-(TRIFLUOROMETHYL)ANILINE - C7 H6 F3 N - 161.124 Da.

1

ANI

Samples:

sample_1: Vpu Cytoplasmic domain, [U-100% 15N], 0.5 mM; DHPC 100 mM; H20 90%; D2O 10%

sample_2: Vpu Cytoplasmic domain, [U-100% 13C; U-100% 15N], 0.5 mM; DHPC 100 mM; H20 90%; D2O 10%

sample_conditions_1: ionic strength: 5 mM; pH: 4.0; pressure: 1 atm; temperature: 323 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D_15N-separated_NOESY	sample_1	isotropic	sample_conditions_1
2D_15N/1N_HSQC	sample_1	isotropic	sample_conditions_1
2D_15N/1N_HSQCIPAP	sample_1	isotropic	sample_conditions_1
3D_HNCA	sample_1	isotropic	sample_conditions_1
3D_HCCCONH	sample_1	isotropic	sample_conditions_1
3D_CCCONH	sample_1	isotropic	sample_conditions_1
3D_15N/13C'/13C	sample_1	isotropic	sample_conditions_1
3D_HNCO	sample_1	isotropic	sample_conditions_1
3D_HNCACB	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

NMR spectrometers:

Bruker AVANCE 600 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts