BMRB Entry 26035

Name: NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of hexafluoroisopropanol
Published: 2017-02-16

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PDB ID: 2nct
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26035
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in the presence of hexafluoroisopropanol PubMed: 27905530

Deposition date: 2016-04-14 Original release date: 2017-02-16

Authors: Jimenez, M. Angeles; Nieva, Jose; Rujas, Edurne; Partida-Hanon, Angelica; Bruix, Marta

Citation: Rujas, Edurne; Partida-Hanon, Angelica; Gulzar, Naveed; Morante, Koldo; Apellaniz, Beatriz; Garcia-Porras, Miguel; Bruix, Marta; Tsumoto, Kouhei; Scott, Jamie; Jimenez, M. Angeles; Caaveiro, Jose; Nieva, Jose. "Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface" Sci Rep 6, 38177-38177 (2016).

Assembly members:
10E8p, polymer, 36 residues, 4624.739 Da.

Natural source: Common Name: HIV-1 Taxonomy ID: 11676 Superkingdom: Viruses Kingdom: not available Genus/species: Lintivirus not available

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
10E8p: KKKKDKWASLWNWFDITNWL WYIKLFIMIVGKKKKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	100
1H chemical shifts	493

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	10E8p	1

Entities:

Entity 1, 10E8p 36 residues - 4624.739 Da.

The sequence DKWASLWNWFDITNWLWYIKLFIMIVG to residues 664-690 of glycoprotein gp41 from HIV. The four N-terminal (KKKK) and the five C-terminal residues (KKKKK) were added to the native sequence to improve peptide solubility.

1

LYS

ASP

LYS

TRP

ALA

SER

LEU

2

TRP

ASN

TRP

PHE

ASP

ILE

THR

ASN

TRP

LEU

3

TRP

TYR

ILE

LYS

LEU

PHE

ILE

MET

ILE

VAL

4

GLY

LYS

Samples:

sample_1: 10E8p 0.5 mM; HFIP, [U-2H], 25 % v/v; HEPES 2 mM; DSS 0.1 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: 10E8p 0.5 mM; HFIP, [U-2H], 25 % v/v; HEPES 2 mM; DSS 0.1 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 2 mM; pH: 7; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 2 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - dihedral angle restraints

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz