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BMRB Entry 30090

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30090
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Title: Structure of the transmembrane domain of HIV-1 gp41 in bicelle

Deposition date: 2016-05-14 Original release date: 2016-06-24

Authors: Dev, J.; Fu, Q.; Park, D.; Chen, B.; Chou, J.

Citation: Dev, J.; Park, D.; Fu, Q.; Chen, J.; Ha, H.; Ghantous, F.; Herrmann, T.; Chang, W.; Liu, Z.; Frey, G.; Seaman, M.; Chen, B.; Chou, J.. "Structural Basis for Membrane Anchoring of HIV-1 Envelope Spike"  .

Assembly members:
Envelope glycoprotein gp160, polymer, 40 residues, 4650.604 Da.

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

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

Entity Sequences (FASTA):
Envelope glycoprotein gp160: NWLWYIRIFIIIVGSLIGLR IVFAVLSLVNRVRQGYSPLS

Data sets:
Data typeCount
13C chemical shifts75
15N chemical shifts37
1H chemical shifts37

Additional metadata:

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

Assembly:

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

Entities:

Entity 1, entity_1, chain 1 40 residues - 4650.604 Da.

1   ASNTRPLEUTRPTYRILEARGILEPHEILE
2   ILEILEVALGLYSERLEUILEGLYLEUARG
3   ILEVALPHEALAVALLEUSERLEUVALASN
4   ARGVALARGGLNGLYTYRSERPROLEUSER

Samples:

sample_1: 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC) 120 ± 3 mM; 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) 60 ± 2 mM; HIV-1 gp41 Transmembrane Domain, [U-13C; U-15N; 85%-2H], 0.8 ± 0.1 mM; MES 25 ± 2 mM; NaN3 0.1 ± 0.01 %

sample_2: 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), acyl chains 2H labeled, 120 ± 3 mM; 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), acyl chains 2H labeled, 60 ± 2 mM; HIV-1 gp41 Transmembrane Domain, [U-13C; U-15N], 0.8 ± 0.1 mM; MES 25 ± 2 mM; NaN3 0.1 ± 0.01 %

sample_3: 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), acyl chains 2H labeled, 120 ± 3 mM; 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), acyl chains 2H labeled, 60 ± 2 mM; HIV-1 gp41 Transmembrane Domain, [U-15N; U-2H], 0.4 ± 0.1 mM; HIV-1 gp41 Transmembrane Domain, [15% 13C], 0.4 ± 0.1 mM; MES 25 ± 2 mM; NaN3 0.1 ± 0.01 %

sample_4: 1,2-Dihexanoyl-sn-Glycero-3-Phosphocholine (DHPC), acyl chains 2H labeled, 120 ± 3 mM; 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC), acyl chains 2H labeled, 60 ± 2 mM; HIV-1 gp41 Transmembrane Domain, [U-15N], 0.8 ± 0.1 mM; MES 25 ± 2 mM; NaN3 0.1 ± 0.01 %

sample_conditions_1: ionic strength: 50 mM; pH: 6.7; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
3D TROSY HNCAsample_1isotropicsample_conditions_1
3D TROSY HNCOCAsample_1isotropicsample_conditions_1
3D TROSY HNCACOsample_1isotropicsample_conditions_1
3D TROSY HNCOsample_1isotropicsample_conditions_1
3D 15N NOESY-TROSY-HSQCsample_2isotropicsample_conditions_1
3D 13C NOESY-HSQC (Methyls)sample_2isotropicsample_conditions_1
3D 15N NOESY-TROSY-HSQC (long mixing time)sample_3isotropicsample_conditions_1
2D 15N TROSY-HSQC for GdDOTA titrationsample_1isotropicsample_conditions_1
3D 15N NOESY-TROSY-HSQC (short mixing time)sample_4isotropicsample_conditions_1

Software:

CcpNMR, CCPN - chemical shift assignment

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

XEASY, Bartels et al. - data analysis

XPLOR-NIH v2.42, G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra - structure calculation

NMR spectrometers:

  • Bruker AvanceII 600 MHz
  • Bruker AvanceII 750 MHz
  • Bruker AvanceIII 900 MHz

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