BMRB Entry 30678

Name: Structure of the HIV-1 gp41 transmembrane domain and cytoplasmic tail (LLP2)
Published: 2020-05-05

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30678

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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: Structure of the HIV-1 gp41 transmembrane domain and cytoplasmic tail (LLP2)

Deposition date: 2019-10-03 Original release date: 2020-05-05

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

Citation: Piai, A.; Fu, Q.; Cai, Y.; Ghantous, F.; Xiao, T.; Shaik, M.; Peng, H.; Rits-Volloch, S.; Liu, Z.; Chen, W.; Seaman, M.; Chen, B.; Chou, J.. "Structural basis of transmembrane coupling of the HIV-1 envelope glycoprotein" Nat. Commun. ., .-..

Assembly members:
entity_1, polymer, 112 residues, 13039.172 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(DE3)

Entity Sequences (FASTA):
entity_1: NWLWYIRIFIIIVGSLIGLR IVFAVLSLVNRVRQGYSPLS FQTHLPTPRGPDRPEGIEEE GGERDRDRSIRLVNGSLALI WDDLRSLSLFSYHRLRDLLL IVTRIVELLGRR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	262
15N chemical shifts	99
1H chemical shifts	99

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, 1 112 residues - 13039.172 Da.

1

ASN

TRP

LEU

TRP

TYR

ILE

ARG

ILE

PHE

ILE

2

ILE

VAL

GLY

SER

LEU

ILE

GLY

LEU

ARG

3

ILE

VAL

PHE

ALA

VAL

LEU

SER

LEU

VAL

ASN

4

ARG

VAL

ARG

GLN

GLY

TYR

SER

PRO

LEU

SER

5

PHE

GLN

THR

HIS

LEU

PRO

THR

PRO

ARG

GLY

6

PRO

ASP

ARG

PRO

GLU

GLY

ILE

GLU

7

GLY

GLU

ARG

ASP

ARG

ASP

ARG

SER

ILE

8

ARG

LEU

VAL

ASN

GLY

SER

LEU

ALA

LEU

ILE

9

TRP

ASP

LEU

ARG

SER

LEU

SER

LEU

PHE

10

SER

TYR

HIS

ARG

LEU

ARG

ASP

LEU

11

ILE

VAL

THR

ARG

ILE

VAL

GLU

LEU

GLY

12

ARG

Samples:

sample_1: HIV-1 gp41 TMD-CT(LLP2), [U-13C; U-15N; U-85% 2H], 0.7 mM; MES 40 mM; DMPC 40 mM; DHPC 80 mM

sample_2: HIV-1 gp41 TMD-CT(LLP2), [U-15N; U-2H], 0.8 mM; MES 40 mM; DMPC 40 mM; DHPC 80 mM

sample_3: HIV-1 gp41 TMD-CT(LLP2), [U-13C; U-15N], 1.0 mM; MES 40 mM; DMPC 40 mM; DHPC 80 mM

sample_4: HIV-1 gp41 TMD-CT(LLP2), [U-15N; U-2H], 0.5 mM; MES 40 mM; DMPC 40 mM; DHPC 80 mM

sample_5: HIV-1 gp41 TMD-CT(LLP2), [U-13C], 0.5 mM; MES 40 mM; DMPC 40 mM; DHPC 80 mM; HIV-1 gp41 TMD-CT (LLP2), [U-15N; U-2H], 0.5 mM

sample_6: HIV-1 gp41 TMD-CT(LLP2), [U-15N; U-85% 2H], 0.5 mM; MES 40 mM; DMPC 40 mM; DHPC 80 mM

sample_conditions_1: 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 TROSY HNCO	sample_1	isotropic	sample_conditions_1
3D TROSY HNCA	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_1	isotropic	sample_conditions_1
3D TROSY HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D TROSY HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D TROSY HNCACB	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_2	isotropic	sample_conditions_1
3D 15N-edited NOESY-TROSY-HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D 15N-edited NOESY-TROSY-HSQC	sample_3	isotropic	sample_conditions_1
3D 13C-edited NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_4	isotropic	sample_conditions_1
3D 15N-edited NOESY-TROSY-HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
3D 15N-edited NOESY-TROSY-HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1
3D J(CH)-modulated NOESY	sample_5	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_6	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

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

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

XEASY, Bartels et al. - chemical shift assignment, peak picking

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

NMR spectrometers:

Bruker AVANCE III HD 600 MHz
Bruker AVANCE III 750 MHz
Bruker AVANCE III 800 MHz
Bruker AVANCE III 900 MHz

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