BMRB Entry 30503

Name: MPER-TM Domain of HIV-1 envelope glycoprotein (Env)
Published: 2018-08-31

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PDB ID: 6e8w
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30503
MolProbity Validation Chart

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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: MPER-TM Domain of HIV-1 envelope glycoprotein (Env) PubMed: 30185554

Deposition date: 2018-07-31 Original release date: 2018-08-31

Authors: Fu, Q.; Shaik, M.; Cai, Y.; Ghantous, F.; Piai, A.; Peng, H.; Rits-Volloch, S.; Liu, Z.; Harrison, S.; Seaman, M.; Chen, B.; Chou, J.

Citation: Fu, Q.; Shaik, M.; Cai, Y.; Ghantous, F.; Piai, A.; Peng, H.; Rits-Volloch, S.; Liu, Z.; Harrison, S.; Seaman, M.; Chen, B.; Chou, J.. "Structure of the membrane proximal external region of HIV-1 envelope glycoprotein" Proc. Natl. Acad. Sci. U.S.A. 115, E8892-E8899 (2018).

Assembly members:
entity_1, polymer, 51 residues, 6179.373 Da.

Natural source: Common Name: HIV-1 Taxonomy ID: 11676 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus HIV-1

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21

Entity Sequences (FASTA):
entity_1: LLELDKWASLWNWFDITNWL WYIRIFIIIVGSLIGLRIVF AVLSLVNRVRQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	88
15N chemical shifts	49
1H chemical shifts	49

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, 1	1
2	entity_1, 2	1
3	entity_1, 3	1

Entities:

Entity 1, entity_1, 1 51 residues - 6179.373 Da.

1

LEU

GLU

LEU

ASP

LYS

TRP

ALA

SER

LEU

2

TRP

ASN

TRP

PHE

ASP

ILE

THR

ASN

TRP

LEU

3

TRP

TYR

ILE

ARG

ILE

PHE

ILE

VAL

4

GLY

SER

LEU

ILE

GLY

LEU

ARG

ILE

VAL

PHE

5

ALA

VAL

LEU

SER

LEU

VAL

ASN

ARG

VAL

ARG

6

GLN

Samples:

sample_1: DMPC 50 mM; DHPC 100 mM; Envelope glycoprotein gp160, 15N, 2H,

sample_2: DMPC 50 mM; DHPC 100 mM; Envelope glycoprotein gp160, [U-13C; U-15N; U-2H],

sample_3: DMPC, [U-99% 2H], 50 mM; DHPC, [U-99% 2H], 100 mM; Envelope glycoprotein gp160, [U-100% 13C; U-100% 15N],

sample_4: DMPC, [U-99% 2H], 50 mM; DHPC, [U-99% 2H], 100 mM; Envelope glycoprotein gp160, 15N, 2H mixed with 13C(15%),

sample_5: DMPC, [U-99% 2H], 50 mM; DHPC, [U-99% 2H], 100 mM; Envelope glycoprotein gp160, 15N, 2H mixed with 13C,

sample_conditions_1: ionic strength: 20 mM; pH: 6.7; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N Trosy HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY tr-HSQC	sample_3	isotropic	sample_conditions_1
3D Jch Modulated 1H-15N NOESY	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY tr-HSQC	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1

Software:

XEASY, Bartels et al. - chemical shift assignment

X-PLOR NIH v2.48, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker AvanceII 800 MHz
Bruker AvanceIII 900 MHz
Bruker AvanceII 600 MHz

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