BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30678

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:
Data typeCount
13C chemical shifts262
15N chemical shifts99
1H chemical shifts99

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_1, 31

Entities:

Entity 1, entity_1, 1 112 residues - 13039.172 Da.

1   ASNTRPLEUTRPTYRILEARGILEPHEILE
2   ILEILEVALGLYSERLEUILEGLYLEUARG
3   ILEVALPHEALAVALLEUSERLEUVALASN
4   ARGVALARGGLNGLYTYRSERPROLEUSER
5   PHEGLNTHRHISLEUPROTHRPROARGGLY
6   PROASPARGPROGLUGLYILEGLUGLUGLU
7   GLYGLYGLUARGASPARGASPARGSERILE
8   ARGLEUVALASNGLYSERLEUALALEUILE
9   TRPASPASPLEUARGSERLEUSERLEUPHE
10   SERTYRHISARGLEUARGASPLEULEULEU
11   ILEVALTHRARGILEVALGLULEULEUGLY
12   ARGARG

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:

NameSampleSample stateSample conditions
2D 1H-15N TROSY-HSQCsample_1isotropicsample_conditions_1
3D TROSY HNCOsample_1isotropicsample_conditions_1
3D TROSY HNCAsample_1isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_1isotropicsample_conditions_1
3D TROSY HN(CA)COsample_1isotropicsample_conditions_1
3D TROSY HN(CO)CAsample_1isotropicsample_conditions_1
3D TROSY HNCACBsample_1isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_2isotropicsample_conditions_1
3D 15N-edited NOESY-TROSY-HSQCsample_2isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D 15N-edited NOESY-TROSY-HSQCsample_3isotropicsample_conditions_1
3D 13C-edited NOESYsample_3isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_4isotropicsample_conditions_1
3D 15N-edited NOESY-TROSY-HSQCsample_4isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
3D 15N-edited NOESY-TROSY-HSQCsample_5isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
3D J(CH)-modulated NOESYsample_5isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_6isotropicsample_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