BMRBj - BMREntryMaster

Found 1 Document (0.479 seconds)

BMRB: 30931

7R95

Membrane bound structure of HR1 domain of SARS-CoV-2 spike protein

Authors

Chiliveri, S.C., Bax, A.

Assembly

Spike protein S2

Entity

1. Spike protein S2 (polymer, Thiol state: not present), 56 monomers, 5923.604 Da Detail

GSWNQKLIAN QFNSAIGKIQ DSLSSTASAL GKLQDVVNQN AQALNTLVKQ SGLVPR

Formula weight

5923.604 Da

Source organism

Severe acute respiratory syndrome coronavirus 2

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 33.2 %, Completeness (bb): 63.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	33.2 % (212 of 638)	16.0 % (53 of 331)	44.7 % (106 of 237)	75.7 % (53 of 70)
Backbone	63.5 % (212 of 334)	46.1 % (53 of 115)	64.6 % (106 of 164)	96.4 % (53 of 55)
Sidechain	0.0 % (0 of 356)	0.0 % (0 of 216)	0.0 % (0 of 125)	0.0 % (0 of 15)
Aromatic	0.0 % (0 of 22)	0.0 % (0 of 11)	0.0 % (0 of 10)	0.0 % (0 of 1)
Methyl	0.0 % (0 of 72)	0.0 % (0 of 36)	0.0 % (0 of 36)

1. entity 1

GSWNQKLIAN QFNSAIGKIQ DSLSSTASAL GKLQDVVNQN AQALNTLVKQ SGLVPR

Show sample condition

Sample #1

Solvent system 97% H2O/3% D2O, Pressure 1 bar, Temperature 308 K, pH 6, Details 0.4 mM [U-13C; U-15N; U-2H] SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 150 mM DMPC/DHPC, 97% H2O/3% D2O

#	Name	Isotope labeling	Concentration
1	SARS-CoV-2 spike protein HR1 domain	[U-13C; U-15N; U-2H]	0.4 mM
2	sodium phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	30 mM
4	DMPC/DHPC	natural abundance	150 mM

Sample #2

Solvent system 97% H2O/3% D2O, Pressure 1 bar, Temperature 308 K, pH 6, Details 0.3 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 150 mM DMPC/DHPC, 97% H2O/3% D2O

#	Name	Isotope labeling	Concentration
5	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.3 mM
6	sodium phosphate buffer	natural abundance	20 mM
7	NaCl	natural abundance	30 mM
8	DMPC/DHPC	natural abundance	150 mM

Sample #3

Solvent system 97% H2O/3% D2O, Pressure 1 bar, Temperature 308 K, pH 6, Details 0.1 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 100 mM DMPC/DHPC, 97% H2O/3% D2O

#	Name	Isotope labeling	Concentration
9	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.1 mM
10	sodium phosphate buffer	natural abundance	20 mM
11	NaCl	natural abundance	30 mM
12	DMPC/DHPC	natural abundance	100 mM

Sample #4

Solvent system 97% H2O/3% D2O, Pressure 1 bar, Temperature 308 K, pH 6, Details 0.15 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 120 mM DMPC/DHPC, 97% H2O/3% D2O

#	Name	Isotope labeling	Concentration
13	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.15 mM
14	sodium phosphate buffer	natural abundance	20 mM
15	NaCl	natural abundance	30 mM
16	DMPC/DHPC	natural abundance	120 mM

Release date

2021-07-25

Citation

Transient lipid-bound states of spike protein heptad repeats provide insights into SARS-CoV-2 membrane fusion
Chiliveri, S.C., Louis, J.M., Ghirlando, R., Bax, A.
Sci. Adv. (2021), 7, eabk2226-eabk2226, PubMed 34623907 , DOI 10.1126/sciadv.abk2226 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 51048 released on 2021-07-29
Title Backbone chemical shift assignments for the post-fusion six-helix bundle (6HB) state of SARS-CoV-2 S2 protein

Related entities 1. Spike protein S2, : 1 : 100 : 44 entities Detail

Experiments performed 10 experiments Detail

1 2D TROSY-HSQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 97% H2O/3% D2O, Pressure 1 bar, Temperature 308 K, pH 6, Details 0.4 mM [U-13C; U-15N; U-2H] SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 150 mM DMPC/DHPC, 97% H2O/3% D2O

#	Name	Isotope labeling	Concentration
1	SARS-CoV-2 spike protein HR1 domain	[U-13C; U-15N; U-2H]	0.4 mM
2	sodium phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	30 mM
4	DMPC/DHPC	natural abundance	150 mM

2 3D HNCO

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SARS-CoV-2 spike protein HR1 domain	[U-13C; U-15N; U-2H]	0.4 mM
2	sodium phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	30 mM
4	DMPC/DHPC	natural abundance	150 mM

3 3D HNCA

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SARS-CoV-2 spike protein HR1 domain	[U-13C; U-15N; U-2H]	0.4 mM
2	sodium phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	30 mM
4	DMPC/DHPC	natural abundance	150 mM

4 3D NOESY-TROSY

Instrument

Bruker AVANCE NEO - 900 MHz

Sample

State isotropic, Solvent system 97% H2O/3% D2O, Pressure 1 bar, Temperature 308 K, pH 6, Details 0.3 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 150 mM DMPC/DHPC, 97% H2O/3% D2O

#	Name	Isotope labeling	Concentration
5	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.3 mM
6	sodium phosphate buffer	natural abundance	20 mM
7	NaCl	natural abundance	30 mM
8	DMPC/DHPC	natural abundance	150 mM

5 2D T1

Instrument

Bruker AVANCE NEO - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
5	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.3 mM
6	sodium phosphate buffer	natural abundance	20 mM
7	NaCl	natural abundance	30 mM
8	DMPC/DHPC	natural abundance	150 mM

6 2D T1rho

Instrument

Bruker AVANCE NEO - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
5	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.3 mM
6	sodium phosphate buffer	natural abundance	20 mM
7	NaCl	natural abundance	30 mM
8	DMPC/DHPC	natural abundance	150 mM

7 2D Het NOE

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.3 mM
6	sodium phosphate buffer	natural abundance	20 mM
7	NaCl	natural abundance	30 mM
8	DMPC/DHPC	natural abundance	150 mM

8 Hydrogen Exchange

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 97% H2O/3% D2O, Pressure 1 bar, Temperature 303 K, pH 7, Details 0.1 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 100 mM DMPC/DHPC, 97% H2O/3% D2O

#	Name	Isotope labeling	Concentration
9	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.1 mM
10	sodium phosphate buffer	natural abundance	20 mM
11	NaCl	natural abundance	30 mM
12	DMPC/DHPC	natural abundance	100 mM

9 1H-15N 2D ARTSY

Instrument

Bruker AVANCE III - 800 MHz

Sample

State anisotropic, Solvent system 97% H2O/3% D2O, Pressure 1 bar, Temperature 308 K, pH 6, Details 0.15 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 120 mM DMPC/DHPC, 97% H2O/3% D2O

#	Name	Isotope labeling	Concentration
13	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.15 mM
14	sodium phosphate buffer	natural abundance	20 mM
15	NaCl	natural abundance	30 mM
16	DMPC/DHPC	natural abundance	120 mM

10 1H-15N E.COSY-TROSY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
13	SARS-CoV-2 spike protein HR1 domain	[U-15N; U-2H]	0.15 mM
14	sodium phosphate buffer	natural abundance	20 mM
15	NaCl	natural abundance	30 mM
16	DMPC/DHPC	natural abundance	120 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30931_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	OK

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr30931_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	212		98.2 (chain: 1, length: 56)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 56, Sequence coverage: 98.2%
- Total number of assignments
  - ¹³C chemical shifts: 106
  - ¹H chemical shifts: 53
  - ¹⁵N chemical shifts: 53
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	237	106	44.7
¹H chemical shifts	331	53	16.0
¹⁵N chemical shifts	70	53	75.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	112	106	94.6
¹H chemical shifts	115	53	46.1
¹⁵N chemical shifts	55	53	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	125	0	0.0
¹H chemical shifts	216	0	0.0
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	36	0	0.0
¹H chemical shifts	36	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	10	0	0.0
¹H chemical shifts	11	0	0.0
¹⁵N chemical shifts	1	0	0.0

Keywords Heptad repeat, SARS-Cov-2, VIRAL PROTEIN, bicelles, lipid-water interface, residual dipolar couplings

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Found 1 Document (0.479 seconds)

BMRB: 30931

Sample #1

Sample #2

Sample #3

Sample #4

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Spike protein S2, : 1 : 100 : 44 entities Detail

Experiments performed 10 experiments Detail

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Chemical shift validation 3 contents Detail