BMRB Entry 30472

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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/BMR30472
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Title:
Oligomeric Structure of the HIV gp41 MPER-TMD in Phospholipid Bilayers
Deposition date:
2018-06-01
Original release date:
2018-08-03
Authors:
Kwon, B.; Lee, M.; Waring, A.; Hong, M.
Citation:

Citation: Kwon, B.; Lee, M.; Waring, A.; Hong, M.. "Oligomeric Structure and Three-Dimensional Fold of the HIV gp41 Membrane-Proximal External Region and Transmembrane Domain in Phospholipid Bilayers"  J. Am. Chem. Soc. 140, 8246-8259 (2018).
PubMed: 29888593

Assembly members:

Assembly members:
entity_1, polymer, 39 residues, 4672.646 Da.

Natural source:

Natural source:   Common Name: isolate HXB2   Taxonomy ID: 11706   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lentivirus HIV-1

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KWASLWNWFNITNWLWYIKL FIMIVGGLVGLRIVFAVLS

Data sets:
Data typeCount
13C chemical shifts23

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

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

Entities:

Entity 1, entity_1, 1 39 residues - 4672.646 Da.

1   LYSTRPALASERLEUTRPASNTRPPHEASN
2   ILETHRASNTRPLEUTRPTYRILELYSLEU
3   PHEILEMETILEVALGLYGLYLEUVALGLY
4   LEUARGILEVALPHEALAVALLEUSER

Samples:

sample_1: HIV gp41 MPER-TMD, 4-19F-F699, 33 ± 5 % w/w; HEPES buffer 10 mM

sample_2: HIV gp41 MPER-TMD, [U-13C; U-15N]-L684,I686, G694, 19F-5F-W678, 19F-4F-F699, 33 ± 5 % w/w; HEPES buffer 10 mM

sample_3: HIV gp41 MPER-TMD, [U-13C; U-15N]-L669,I686, A700, 13C'-G694, 19F-5F-W680, 33 ± 5 % w/w; HEPES buffer 10 mM

sample_conditions_1: pH: 7.5; pressure: 1 atm; temperature: 263 K

sample_conditions_2: pH: 7.5; pressure: 1 atm; temperature: 233 K

Experiments:

NameSampleSample stateSample conditions
2D 13C-13C DARRsample_3isotropicsample_conditions_1
2D water Edited DARRsample_3isotropicsample_conditions_1
13C-19F REDORsample_2isotropicsample_conditions_2
2D water Edited DARRsample_2isotropicsample_conditions_1
19F CODEXsample_1isotropicsample_conditions_2
19F CODEXsample_3isotropicsample_conditions_2
19F CODEXsample_2isotropicsample_conditions_2

Software:

TOPSPIN, Bruker Biospin - chemical shift assignment

Matlab, Mathwork - data analysis

GROMACS, University of GroningenRoyal Institute of TechnologyUppsala University - refinement, structure calculation

CHARMM-GUI, Lehigh University / Department of Biological Sciences / Department of Bioengineering/ Im Lab - refinement, structure calculation

NMR spectrometers:

  • Bruker Bruker 400 MHz
  • Bruker Bruker 600 MHz
  • Bruker Bruker 800 MHz