BMRB Entry 30795

Name: SARS-CoV-2 Envelope Protein Transmembrane Domain: Pentameric Structure Determined by Solid-State NMR
Published: 2020-09-28

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PDB ID: 7k3g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30795
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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:

SARS-CoV-2 Envelope Protein Transmembrane Domain: Pentameric Structure Determined by Solid-State NMR

Deposition date:

2020-09-11

Original release date:

2020-09-28

Authors:

Mandala, V.; Hong, M.; McKay, M.; Shcherbakov, A.; Dregni, A.

Citation:

Citation: Mandala, Venkata; McKay, Matthew; Shcherbakov, Alexander; Dregni, Aurelio; Kolocouris, Antonios; Hong, Mei. "Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers" Nat. Struct. Mol. Biol. 27, 1202-1208 (2020).
PubMed: 33177698

Assembly members:

Assembly members:
entity_1, polymer, 31 residues, 3362.115 Da.

Natural source:

Natural source: Common Name: 2019-nCoV Taxonomy ID: 2697049 Superkingdom: Viruses Kingdom: not available Genus/species: Betacoronavirus HCoV-SARS

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: ETGTLIVNSVLLFLAFVVFL LVTLAILTALR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	133
15N chemical shifts	28

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1
3	unit_3	1
4	unit_4	1
5	unit_5	1

Entities:

Entity 1, unit_1 31 residues - 3362.115 Da.

1

GLU

THR

GLY

THR

LEU

ILE

VAL

ASN

SER

VAL

2

LEU

PHE

LEU

ALA

PHE

VAL

PHE

LEU

3

LEU

VAL

THR

LEU

ALA

ILE

LEU

THR

ALA

LEU

4

ARG

Samples:

sample_1: SARS-CoV-2 Envelope Protein Transmembrane Domain, [U-13C; U-15N], 0.1 mg/uL; POPC 0.23 mg/uL; POPE 0.1 mg/uL; bovine PI 0.08 mg/uL; POPS 0.04 mg/uL; Cholesterol 0.04 mg/uL

sample_2: SARS-CoV-2 Envelope Protein Transmembrane Domain, [U-13C; U-15N], 0.1 mg/uL; POPC 0.23 mg/uL; POPE 0.1 mg/uL; bovine PI 0.08 mg/uL; POPS 0.04 mg/uL; Cholesterol 0.04 mg/uL; fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain, [4-19F-Phe], 0.1 mg/uL

sample_3: POPC 0.23 mg/uL; POPE 0.1 mg/uL; bovine PI 0.08 mg/uL; POPS 0.04 mg/uL; Cholesterol 0.04 mg/uL; 15N SARS-CoV-2 Envelope Protein Transmembrane Domain, [U-15N], 0.1 mg/uL; 13C SARS-CoV-2 Envelope Protein Transmembrane Domain, [U-13C], 0.1 mg/uL

sample_conditions_1: ionic strength: 20 mM; pH: 7.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D CC CORD	sample_1	anisotropic	sample_conditions_1
2D NCA/NCO SPEC-CP	sample_1	anisotropic	sample_conditions_1
3D NCACX/NCOCX/CONCA	sample_1	anisotropic	sample_conditions_1
1D/2D 13C-19F REDOR	sample_2	anisotropic	sample_conditions_1
2D 13C-19F SPEC-CP	sample_2	anisotropic	sample_conditions_1
2D NHHC	sample_3	anisotropic	sample_conditions_1

Software:

NMRFAM-SPARKY, NMRFAM - chemical shift assignment

TopSpin, Bruker Biospin - processing

X-PLOR NIH v2.47, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE NEO 900 MHz
Bruker AVANCE II 800 MHz
Bruker AVANCE III HD 60 MHz