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In response to the declaration of global pandemic of Coronavirus infectious disease 2019 (COVID-19) caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we provide comprehensive content on Coronavirus molecular structures and its interactions:

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BMRB: 16981

2KYS

NMR Structure of the SARS Coronavirus Nonstructural Protein Nsp7 in Solution at pH 6.5

Authors

Johnson, M.A., Jaudzems, K., Wuthrich, K.

Assembly

SARS Coronavirus Nonstructural Protein Nsp7

Entity

1. SARS Coronavirus Nonstructural Protein Nsp7 (polymer, Thiol state: all free), 85 monomers, 9461.933 Da Detail

GHSKMSDVKC TSVVLLSVLQ QLRVESSSKL WAQCVQLHND ILLAKDTTEA FEKMVSLLSV LLSMQGAVDI NRLCEEMLDN RATLQ

Formula weight

9461.933 Da

Source organism

Severe acute respiratory syndrome-related coronavirus

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.5 %, Completeness (bb): 84.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (897 of 980)	99.0 % (500 of 505)	80.0 % (304 of 380)	97.9 % (93 of 95)
Backbone	84.7 % (432 of 510)	98.8 % (170 of 172)	70.8 % (179 of 253)	97.6 % (83 of 85)
Sidechain	99.1 % (548 of 553)	99.1 % (330 of 333)	99.0 % (208 of 210)	100.0 % (10 of 10)
Aromatic	93.3 % (28 of 30)	100.0 % (15 of 15)	85.7 % (12 of 14)	100.0 % (1 of 1)
Methyl	100.0 % (122 of 122)	100.0 % (61 of 61)	100.0 % (61 of 61)

1. nsp7

GHSKMSDVKC TSVVLLSVLQ QLRVESSSKL WAQCVQLHND ILLAKDTTEA FEKMVSLLSV LLSMQGAVDI NRLCEEMLDN RATLQ

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

LACS Plot; CA

Referencing offset: 0.12 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.12 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.17 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KYS, Strand ID: A Detail

Release date

2010-07-07

Citation

NMR Structure of the SARS-CoV Nonstructural Protein 7 in Solution at pH 6.5
Johnson, M.A., Jaudzems, K., Wuthrich, K.
J. Mol. Biol. (2010), 402, 619-628, PubMed 20709084 , DOI 10.1016/j.jmb.2010.07.043 , Abstract

Related entities 1. SARS Coronavirus Nonstructural Protein Nsp7, : 1 : 1 : 5 : 140 entities Detail

Experiments performed 9 experiments Detail

1 3D 15N-resolved [1H,1H]-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

2 3D 13C-resolved [1H,1H]-NOESY (aliphatic carbons)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

3 3D 13C-resolved [1H,1H]-NOESY (aromatic carbons)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

4 2D [15N,1H]-HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

6 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

8 3D HC(C)H-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

9 2D [13C,1H]-HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	nsp7	[U-98% 13C; U-98% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		10 mM
5	sodium azide	natural abundance		3 mM
6	H2O	natural abundance		93 %
7	D2O	natural abundance		7 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16981_2kys.nef
Input source #2: Coordindates	2kys.cif
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

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80-----
GHSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRATLQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINRLCEEMLDNRATLQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_16981_2kys.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	886		100.0 (chain: A, length: 85)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2360 (1)	noe	100.0 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 500
  - ¹³C chemical shifts: 293
  - ¹⁵N chemical shifts: 93
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Tautomeric state of HIS
- 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: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 100.0%
- Total number of restraints: 2360
- Weight of restraints: 1.0 (2360)
- Potential type of restraints: upper-bound-parabolic (2360)
- Range of distance target values: 2.43, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords conformational polymorphism, coronavirus, nsp7, severe acute respiratory syndrome (SARS)