BMRB Entry 34130

Name: NMR assignment and structure of a peptide derived from the fusion peptide of HIV-1 gp41 in the presence of dodecylphosphocholine micelles
Published: 2017-11-28

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PDB ID: 5nvp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34130
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
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 fusion peptide of HIV-1 gp41 in the presence of dodecylphosphocholine micelles

Deposition date:

2017-05-04

Original release date:

2017-11-28

Authors:

Jimenez, M.; Serrano, S.; Nieva, J.; Huarte, N.

Citation:

Citation: Serrano, S.; Huarte, N.; Rujas, E.; Andreu, D.; Nieva, J.; Jimenez, M.. "Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance" Biochemistry 56, 5503-5511 (2017).
PubMed: 28930470

Assembly members:

Assembly members:
entity_1, polymer, 35 residues, 3822.411 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GIGALFLGFLGAAGSKKXKN EQELLELDKWASLWN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	45
1H chemical shifts	258

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 35 residues - 3822.411 Da.

1

GLY

ILE

GLY

ALA

LEU

PHE

LEU

GLY

PHE

LEU

2

GLY

ALA

GLY

SER

LYS

ACA

LYS

ASN

3

GLU

GLN

GLU

LEU

GLU

LEU

ASP

LYS

TRP

4

ALA

SER

LEU

TRP

ASN

Samples:

sample_1: D2O, [U-99% 2H], 10%; DPC, [U-98% 2H], 20 mM; DSS 0.1 mM; H2O 90%; HEPES 2.0 mM; wtFP-tag 0.6 ± 0.1 mM

sample_conditions_1: ionic strength: 2 mM; pH: 6.8 pH*; 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:

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection, processing

NMR spectrometers:

Bruker Avance 600 MHz