BMRBj - BMREntryMaster

Found 1 Document (0.612 seconds)

BMRB: 30795

2MM4

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

Authors

Mandala, V.S., Hong, M., McKay, M.J., Shcherbakov, A.S., Dregni, A.J.

Assembly

Envelope small membrane protein

Entity

1. Envelope small membrane protein (polymer, Thiol state: not present), 31 monomers, 3361.105 × 5 Da Detail

ETGTLIVNSV LLFLAFVVFL LVTLAILTAL R

Total weight

16805.525 Da

Max. entity weight

3361.105 Da

Source organism

Severe acute respiratory syndrome coronavirus 2

Exptl. method

solid-state NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 82.1 %, Completeness (bb): 91.1 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	82.1 % (156 of 190)	81.5 % (128 of 157)	84.8 % (28 of 33)
Backbone	91.1 % (112 of 123)	92.4 % (85 of 92)	87.1 % (27 of 31)
Sidechain	74.2 % (72 of 97)	74.7 % (71 of 95)	50.0 % (1 of 2)
Aromatic	0.0 % (0 of 15)	0.0 % (0 of 15)
Methyl	87.2 % (34 of 39)	87.2 % (34 of 39)

1. entity 1

ETGTLIVNSV LLFLAFVVFL LVTLAILTAL R

Show sample condition

Sample #1

Solvent system aqueous buffer, Pressure 1 atm, Temperature 293 K, pH 7.5 (±0.2), Details 0.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer.

#	Name	Isotope labeling	Concentration
1	SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C; U-15N]	0.1 mg/uL
2	POPC	natural abundance	0.23 mg/uL
3	POPE	natural abundance	0.1 mg/uL
4	bovine PI	natural abundance	0.08 mg/uL
5	POPS	natural abundance	0.04 mg/uL
6	Cholesterol	natural abundance	0.04 mg/uL

Sample #2

Solvent system aqueous buffer, Pressure 1 atm, Temperature 293 K, pH 7.5 (±0.2), Details 0.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [4-19F-Phe] fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer.

#	Name	Isotope labeling	Concentration
7	SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C; U-15N]	0.1 mg/uL
8	POPC	natural abundance	0.23 mg/uL
9	POPE	natural abundance	0.1 mg/uL
10	bovine PI	natural abundance	0.08 mg/uL
11	POPS	natural abundance	0.04 mg/uL
12	Cholesterol	natural abundance	0.04 mg/uL
13	fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain	[4-19F-Phe]	0.1 mg/uL

Sample #3

Solvent system aqueous buffer, Pressure 1 atm, Temperature 293 K, pH 7.5 (±0.2), Details 0.1 mg/uL [U-15N] 15N SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [U-13C] 13C SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer.

#	Name	Isotope labeling	Concentration
14	POPC	natural abundance	0.23 mg/uL
15	POPE	natural abundance	0.1 mg/uL
16	bovine PI	natural abundance	0.08 mg/uL
17	POPS	natural abundance	0.04 mg/uL
18	Cholesterol	natural abundance	0.04 mg/uL
19	15N SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-15N]	0.1 mg/uL
20	13C SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C]	0.1 mg/uL

Protein Blocks Logo

Calculated from 10 models in PDB: 7K3G, Strand ID: A, B, C, D, E Detail

Release date

2020-09-21

Citation

Structure and Drug Binding of the SARS-CoV-2 Envelope Protein in Phospholipid Bilayers
Mandala, V.S., McKay, M.J., Shcherbakov, A.A., Dregni, A.J., Kolocouris, A., Hong, M.
Res. Sq. (2020), 27, 1202-1208, PubMed 32995764 , DOI 10.21203/rs.3.rs-77124/v1 , Abstract

Related entities 1. Envelope small membrane protein, : 1 : 4 : 1 : 7 entities Detail

Experiments performed 6 experiments Detail

1 2D CC CORD

Instrument

Bruker AVANCE NEO - 900 MHz

Sample

State anisotropic, Solvent system aqueous buffer, Pressure 1 atm, Temperature 293 K, pH 7.5 (±0.2), Details 0.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer.

#	Name	Isotope labeling	Concentration
1	SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C; U-15N]	0.1 mg/uL
2	POPC	natural abundance	0.23 mg/uL
3	POPE	natural abundance	0.1 mg/uL
4	bovine PI	natural abundance	0.08 mg/uL
5	POPS	natural abundance	0.04 mg/uL
6	Cholesterol	natural abundance	0.04 mg/uL

2 2D NCA/NCO SPEC-CP

Instrument

Bruker AVANCE NEO - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C; U-15N]	0.1 mg/uL
2	POPC	natural abundance	0.23 mg/uL
3	POPE	natural abundance	0.1 mg/uL
4	bovine PI	natural abundance	0.08 mg/uL
5	POPS	natural abundance	0.04 mg/uL
6	Cholesterol	natural abundance	0.04 mg/uL

3 3D NCACX/NCOCX/CONCA

Instrument

Bruker AVANCE NEO - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C; U-15N]	0.1 mg/uL
2	POPC	natural abundance	0.23 mg/uL
3	POPE	natural abundance	0.1 mg/uL
4	bovine PI	natural abundance	0.08 mg/uL
5	POPS	natural abundance	0.04 mg/uL
6	Cholesterol	natural abundance	0.04 mg/uL

4 1D/2D 13C-19F REDOR

Instrument

Bruker AVANCE III HD - na MHz

Sample

State anisotropic, Solvent system aqueous buffer, Pressure 1 atm, Temperature 293 K, pH 7.5 (±0.2), Details 0.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [4-19F-Phe] fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer.

#	Name	Isotope labeling	Concentration
7	SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C; U-15N]	0.1 mg/uL
8	POPC	natural abundance	0.23 mg/uL
9	POPE	natural abundance	0.1 mg/uL
10	bovine PI	natural abundance	0.08 mg/uL
11	POPS	natural abundance	0.04 mg/uL
12	Cholesterol	natural abundance	0.04 mg/uL
13	fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain	[4-19F-Phe]	0.1 mg/uL

5 2D 13C-19F SPEC-CP

Instrument

Bruker AVANCE III HD - na MHz

Sample

State anisotropic, Solvent system aqueous buffer, Pressure 1 atm, Temperature 293 K, pH 7.5 (±0.2), Details 0.1 mg/uL [U-13C; U-15N] SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [4-19F-Phe] fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer.

#	Name	Isotope labeling	Concentration
7	SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C; U-15N]	0.1 mg/uL
8	POPC	natural abundance	0.23 mg/uL
9	POPE	natural abundance	0.1 mg/uL
10	bovine PI	natural abundance	0.08 mg/uL
11	POPS	natural abundance	0.04 mg/uL
12	Cholesterol	natural abundance	0.04 mg/uL
13	fluoro SARS-CoV-2 Envelope Protein Transmembrane Domain	[4-19F-Phe]	0.1 mg/uL

6 2D NHHC

Instrument

Bruker AVANCE II - 800 MHz

Sample

State anisotropic, Solvent system aqueous buffer, Pressure 1 atm, Temperature 293 K, pH 7.5 (±0.2), Details 0.1 mg/uL [U-15N] 15N SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.1 mg/uL [U-13C] 13C SARS-CoV-2 Envelope Protein Transmembrane Domain, 0.23 mg/uL POPC, 0.1 mg/uL POPE, 0.08 mg/uL bovine PI, 0.04 mg/uL POPS, 0.04 mg/uL Cholesterol, aqueous buffer.

#	Name	Isotope labeling	Concentration
14	POPC	natural abundance	0.23 mg/uL
15	POPE	natural abundance	0.1 mg/uL
16	bovine PI	natural abundance	0.08 mg/uL
17	POPS	natural abundance	0.04 mg/uL
18	Cholesterol	natural abundance	0.04 mg/uL
19	15N SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-15N]	0.1 mg/uL
20	13C SARS-CoV-2 Envelope Protein Transmembrane Domain	[U-13C]	0.1 mg/uL

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30795_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30795_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	161		93.5 (chain: 1, length: 31)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 31, Sequence coverage: 93.5%
- Total number of assignments
  - ¹³C chemical shifts: 133
  - ¹⁵N chemical shifts: 28
- Completeness of assignments
  - Entity_assemble_ID: 1
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
8	ASN	CG	174.22
13	PHE	CG	138.4
16	PHE	CG	139.24
19	PHE	CG	139.04
31	ARG	CZ	159.43

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	157	128	81.5
¹⁵N chemical shifts	33	28	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	62	57	91.9
¹⁵N chemical shifts	31	27	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	95	71	74.7
¹⁵N chemical shifts	2	1	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	39	34	87.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	15	0	0.0

Keywords Pentameric Ion Channel, Transmembrane Domain, VIRAL PROTEIN, Viroporin

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.612 seconds)

BMRB: 30795

Sample #1

Sample #2

Sample #3

Related entities 1. Envelope small membrane protein, : 1 : 4 : 1 : 7 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail