BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 19582

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

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:
CpreTM, polymer, 28 residues, 3489.345 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):
CpreTM: KKKNWFDITNWLWYIKLFIM IVGGLVKK

Data sets:
Data typeCount
13C chemical shifts87
1H chemical shifts243

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1CpreTM1

Entities:

Entity 1, CpreTM 28 residues - 3489.345 Da.

The sequence NWFDITNWLWYIKLFIMIVGGLVK corresponds to residues 656-683 of glycoprotein gp41 from HIV. The three N-terminal residues (KKK) and the C-terminal K were added to the native sequence to improve peptide solubility.

1   LYSLYSLYSASNTRPPHEASPILETHRASN
2   TRPLEUTRPTYRILELYSLEUPHEILEMET
3   ILEVALGLYGLYLEUVALLYSLYS

Samples:

sample_1: CpreTM 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:

BMRB 19583
PDB
GB AAC58893 AAD12142 AAS72624 AAV28703 AAV39368