BMRB Entry 19262

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: 2014-01-21

Click here to enlarge.

PDB ID: 2m8m
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19262
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

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:

2013-05-23

Original release date:

2014-01-21

Authors:

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

Citation:

Citation: Serrano, Soraya; Araujo, Aitziber; Apellaniz, Beatriz; de la Arada, Igor; Huarte, Nerea; Arrondo, Jose; Jimenez, M. Angeles; Nieva, Jose. "Structure and immunogenicity of a peptide vaccine based on the membrane proximal external region of HIV-1 gp41" .

Assembly members:

Assembly members:
MPERp, polymer, 28 residues, 3656.148 Da.

Natural source:

Natural source: Common Name: HIV Taxonomy ID: 11676 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human Immunodeficiency Virus 1

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MPERp: NEQELLELDKWASLWNWFNI TNWLWYIK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	18
1H chemical shifts	222

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MPERp-1	1

Entities:

Entity 1, MPERp-1 28 residues - 3656.148 Da.

1

ASN

GLU

GLN

GLU

LEU

GLU

LEU

ASP

LYS

2

TRP

ALA

SER

LEU

TRP

ASN

TRP

PHE

ASN

ILE

3

THR

ASN

TRP

LEU

TRP

TYR

ILE

LYS

Samples:

sample_1: MPERp 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	15605 18237 19215 19263
PDB	1JAU 1JAV 2LP7 2M7W 2M8M 2M8O 2PV6 2X7R 3D0L 3DRQ 3DRT 3EGS 3G9R 3GWO 3H00 3H01 3MNW
DBJ	BAA12995 BAA13003 BAD66665 BAF34648 BAH97413
EMBL	CAA25903 CAA77628 CAI79675 CAI79676 CAI79677
GB	AAA19136 AAA19137 AAA19138 AAA19139 AAA19148
PIR	VCLJSC
PRF	1102247A
REF	NP_057856 NP_579895
SP	P03375 P03377 P04578 P04582 P04624
AlphaFold	P03375 P03377 P04578 P04582 P04624