BMRB Entry 19750

Name: Solution NMR structure of gp41 ectodomain monomer on a DPC micelle
Published: 2014-02-17

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PDB ID: 2mk3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19750
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR structure of gp41 ectodomain monomer on a DPC micelle PubMed: 24550514

Deposition date: 2014-01-23 Original release date: 2014-02-17

Authors: Roche, Julien; Louis, John; Grishaev, Alexander; Ying, Jinfa; Bax, Adriaan

Citation: Roche, Julien; Louis, John; Grishaev, Alexander; Ying, Jinfa; Bax, Adriaan. "Dissociation of the trimeric gp41 ectodomain at the lipid-water interface suggests an active role in HIV-1 Env-mediated membrane fusion." Proc. Natl. Acad. Sci. U.S.A. 111, 3425-3430 (2014).

Assembly members:
entity, polymer, 72 residues, 7879.830 Da.

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

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

Entity Sequences (FASTA):
entity: GSHMSGIVQQQNNLLRAIEA QQHLLQLTVWGIKQLQARSG GRGGWMEWDREINNYTSLIH SLIEESQNQQEK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	195
15N chemical shifts	68
1H chemical shifts	125

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	gp41 ectodomain monomer	1

Entities:

Entity 1, gp41 ectodomain monomer 72 residues - 7879.830 Da.

1

GLY

SER

HIS

MET

SER

GLY

ILE

VAL

GLN

2

GLN

ASN

LEU

ARG

ALA

ILE

GLU

ALA

3

GLN

HIS

LEU

GLN

LEU

THR

VAL

TRP

4

GLY

ILE

LYS

GLN

LEU

GLN

ALA

ARG

SER

GLY

5

GLY

ARG

GLY

TRP

MET

GLU

TRP

ASP

ARG

6

GLU

ILE

ASN

TYR

THR

SER

LEU

ILE

HIS

7

SER

LEU

ILE

GLU

SER

GLN

ASN

GLN

8

GLU

LYS

Samples:

Isotropic_sample: DPC, [U-99% 2H], 100 mM; sodium phosphate 50 mM; H2O 93%; D2O 7%; gp41 ectodomain monomer, [U-2H; U-15N; U-13C],

Aligned_sample: DPC, [U-99% 2H], 100 mM; potassium phosphate 50 mM; H2O 93%; D2O 7%; gp41 ectodomain monomer, [U-2H; U-15N; U-13C], ; acrylamide gel 5.5%; cationic DADMAC-acrylamide copolymer 30%

sample_conditions_1: ionic strength: 0.05 M; pH: 4.0; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	Isotropic_sample	isotropic	sample_conditions_1
3D HNCO	Isotropic_sample	isotropic	sample_conditions_1
3D 1H-15N NOESY	Isotropic_sample	isotropic	sample_conditions_1
3D HCCH-TOCSY	Isotropic_sample	isotropic	sample_conditions_1
2D 1H-1H NOESY	Isotropic_sample	isotropic	sample_conditions_1
2D 1H-15N Artsy	Aligned_sample	anisotropic	sample_conditions_1
2D 1H-15N Trosy-HSQC	Aligned_sample	anisotropic	sample_conditions_1
3D HNCO	Aligned_sample	anisotropic	sample_conditions_1

Software:

X-PLOR_NIH v2.34, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz
Bruker Avance 900 MHz
Bruker Avance 500 MHz

Biological Magnetic Resonance Data Bank