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 19581

Title: NMR assignment and structure of a peptide derived from the trans-membrane region of HIV-1 gp41 in the presence of hexafluoroisopropanol

Deposition date: 2013-10-24 Original release date: 2015-03-23

Authors: Serrano, Soraya; Apellaniz, Beatriz; Huarte, Nerea; Nieva, Jose; Jimenez, M. Angeles

Citation: Serrano, Soraya; Apellaniz, Beatriz; Huarte, Nerea; Jimenez, M. Angeles; Nieva, Jose. "The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and its Connection to the Inmmunogenic Membrane-proximal External Region"  Not known ., .-..

Assembly members:
TMDp, polymer, 27 residues, 3006.957 Da.

Natural source:   Common Name: HIV   Taxonomy ID: 12721   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lentivirus Human immunodeficiency virus

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
TMDp: KKKLFIMIVGGLVGLRIVFA VLSIKKK

Data sets:
Data typeCount
13C chemical shifts94
1H chemical shifts231

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1peptide derived from the trans-membrane region of HIV-1 gp411

Entities:

Entity 1, peptide derived from the trans-membrane region of HIV-1 gp41 27 residues - 3006.957 Da.

Residues KLFIMIVGGLVGLRIVFAVLSI correspond to residues 683-704 of glycoprotein gp41 from HIV. The two N-terminal residues (KK) and the three C-terminal residues (KKK) were added to increase peptide solubility.

1   LYSLYSLYSLEUPHEILEMETILEVALGLY
2   GLYLEUVALGLYLEUARGILEVALPHEALA
3   VALLEUSERILELYSLYSLYS

Samples:

sample_1: TMDp 0.5 mM; H2O 67.5%; D2O, [U-100% 2H], 7.5%; hexafluoroisopropanol 25%; HEPES 2 mM; DSS 0.1 mM

sample_conditions_1: ionic strength: 2 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAD66665 BAF34648 BAK48604
EMBL CAD10141
GB AAA44661 AAA44992 AAB50262 AAB59873 AAB60578
PRF 1103299B
REF NP_057856 NP_579895
SP P04578 P04582