BMRB Entry 19582

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: 2015-03-23

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PDB ID: 2mg2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19582
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Nicholas Rego and David Koes
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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

Deposition date:

2013-10-24

Original release date:

2015-03-23

Authors:

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

Citation:

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" .

Assembly members:

Assembly members:
CpreTM, polymer, 28 residues, 3489.345 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CpreTM: KKKNWFDITNWLWYIKLFIM IVGGLVKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	87
1H chemical shifts	243

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CpreTM	1

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

LYS

ASN

TRP

PHE

ASP

ILE

THR

ASN

2

TRP

LEU

TRP

TYR

ILE

LYS

LEU

PHE

ILE

MET

3

ILE

VAL

GLY

LEU

VAL

LYS

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:

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

BMRB	19583
PDB	2MG2 2MG3
GB	AAC58893 AAD12142 AAS72624 AAV28703 AAV39368