BMRB Entry 19514

Name: HIV-1 gp41 clade C Membrane Proximal External Region peptide in DPC micelle
Published: 2013-10-08

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PDB ID: 2me3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19514
MolProbity Validation Chart

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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:

HIV-1 gp41 clade C Membrane Proximal External Region peptide in DPC micelle

Deposition date:

2013-09-20

Original release date:

2013-10-08

Authors:

Sun, Zhenyu; Wagner, Gerhard; Reinherz, Ellis; Kim, Mikyung; Song, Likai; Choi, Jaewon; Cheng, Yuxing; Chowdhury, Barnali; Bellot, Gaetan; Shih, William

Citation:

Citation: Sun, Zhen-Yu; Cheng, Yuxing; Kim, Mikyung; Song, Likai; Choi, Jaewon; Kudahl, Ulrich; Brusic, Vladimir; Chowdhury, Barnali; Yu, Lu; Seaman, Michael; Bellot, Gaetan; Shih, William; Wagner, Gerhard; Reinherz, Ellis. "Disruption of helix-capping residues 671 and 674 reveals a role in HIV-1 entry for a specialized hinge segment of the membrane proximal external region of gp41." J. Mol. Biol. 426, 1095-1108 (2014).
PubMed: 24075869

Assembly members:

Assembly members:
MPER-Du151, polymer, 27 residues, 3514.057 Da.

Natural source:

Natural source: Common Name: Human immunodeficiency virus 1 Taxonomy ID: 388796 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human immunodeficiency virus 1

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET31

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MPER-Du151: EKDLLALDSWKNLWNWFNIT NWLWYIK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	112
15N chemical shifts	34
1H chemical shifts	224

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MPER-Du151	1

Entities:

Entity 1, MPER-Du151 27 residues - 3514.057 Da.

hiv-1 clade C MPER sequence from Du151.2. Residues 657-661 are from gp41 CHR.

1

GLU

LYS

ASP

LEU

ALA

LEU

ASP

SER

TRP

2

LYS

ASN

LEU

TRP

ASN

TRP

PHE

ASN

ILE

THR

3

ASN

TRP

LEU

TRP

TYR

ILE

LYS

Samples:

sample_1: MPER-Du151, [U-100% 13C; U-100% 15N], 1 mM; DPC, [U-100% 2H], 100 mM; H2O 90%; D20 10%

sample_2: MPER-Du151, [U-100% 15N], 1 mM; DPC, [U-100% 2H], 100 mM; H2O 90%; D20 10%

sample_3: MPER-Du151 1 mM; DPC, [U-100% 2H], 100 mM; D2O 100%

sample_4: MPER-Du151, [U-100% 13C; U-100% 15N], 1 mM; DPC, [U-100% 2H], 100 mM; DNA nanotube 20 mg/mL; H2O 90%; D20 10%

sample_conditions_1: pH: 6.6; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D backbone	sample_1	isotropic	sample_conditions_1
3D C(CO)NH,H(CCO)NH,HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY,TOCSY	sample_3	isotropic	sample_conditions_1
Q-J RDC	sample_4	anisotropic	sample_conditions_1

Software:

NMRPipe v9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CARA v1.8.4, Rochus Keller - chemical shift assignment, data analysis, peak picking

TALOS v+, (TALOS+) Shen, Cornilescu, Delaglio and Bax - data analysis

CYANA v3.0c, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH v2.28, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 750 MHz
Bruker Avance 600 MHz
Varian INOVA 600 MHz

GB	DQ411851 AAF82013 AAL66552 AAL66596 AAL66597 AAO50446
PDB	2ME3
DBJ	BAC77500