BMRBj - BMREntryMaster

Found 1 Document (0.65 seconds)

BMRB: 34661

Structure of SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a

Authors

Bessa, L.M., Guseva, S., Camacho-Zarco, A.R., Salvi, N., Blackledge, M.

Assembly

3C-like proteinase (E.C.3.4.19.12,3.4.22.69), Nucleoprotein

Entity

1. 3C-like proteinase (E.C.3.4.19.12,3.4.22.69), Nucleoprotein, entity 1 (polymer), 96 monomers, 10886.12 Da Detail

QGYKSVNITF ELDERIDKVL NEKCSAYTVE LGTEVNEFAC VVADAVIKTL QPVSELLTPL GIDLDEWSMA TYYLFDESGE FKLASHMYCS FYPPDE

2. 3C-like proteinase (E.C.3.4.19.12,3.4.22.69), Nucleoprotein, entity 2 (polymer), 73 monomers, 7696.535 Da Detail

RNSSRNSTPG SSRGTSPARM AGNGGDAALA LLLLDRLNQL ESKMSGKGQQ QQGQTVTKKS AAEASKKPRQ KRT

Total weight

18582.656 Da

Max. entity weight

10886.12 Da

Source organism

Severe acute respiratory syndrome coronavirus 2

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 52.4 %, Completeness (bb): 66.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.4 % (1010 of 1926)	48.6 % (486 of 1000)	49.4 % (365 of 739)	85.0 % (159 of 187)
Backbone	66.4 % (664 of 1000)	76.7 % (263 of 343)	49.3 % (244 of 495)	96.9 % (157 of 162)
Sidechain	41.1 % (445 of 1083)	34.1 % (224 of 657)	54.6 % (219 of 401)	8.0 % (2 of 25)
Aromatic	4.4 % (5 of 114)	3.5 % (2 of 57)	3.6 % (2 of 56)	100.0 % (1 of 1)
Methyl	70.0 % (119 of 170)	68.2 % (58 of 85)	71.8 % (61 of 85)

1. entity 1

QGYKSVNITF ELDERIDKVL NEKCSAYTVE LGTEVNEFAC VVADAVIKTL QPVSELLTPL GIDLDEWSMA TYYLFDESGE FKLASHMYCS FYPPDE

2. entity 2

RNSSRNSTPG SSRGTSPARM AGNGGDAALA LLLLDRLNQL ESKMSGKGQQ QQGQTVTKKS AAEASKKPRQ KRT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-15N] sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	sN3	[U-15N]	500 uM
2	sUbl1	natural abundance	550 uM
3	sodium phosphate	natural abundance	50 mM
4	sodium chloride	natural abundance	250 mM
5	DTT	natural abundance	2 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-13C; U-15N] sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	sN3	[U-13C; U-15N]	500 uM
7	sUbl1	natural abundance	550 uM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	250 mM
10	DTT	natural abundance	2 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-15N] sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sN3	natural abundance	550 uM
12	sUbl1	[U-15N]	500 uM
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	250 mM
15	DTT	natural abundance	2 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-13C; U-15N] sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
16	sN3	natural abundance	550 uM
17	sUbl1	[U-13C; U-15N]	500 uM
18	sodium phosphate	natural abundance	50 mM
19	sodium chloride	natural abundance	250 mM
20	DTT	natural abundance	2 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM 100% A220I Cd1 13C sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	sN3	natural abundance	550 uM
22	sUbl1	100% A220I Cd1 13C	500 uM
23	sodium phosphate	natural abundance	50 mM
24	sodium chloride	natural abundance	250 mM
25	DTT	natural abundance	2 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
26	sN3	natural abundance	500 uM
27	sUbl1	natural abundance	550 uM
28	sodium phosphate	natural abundance	50 mM
29	sodium chloride	natural abundance	250 mM
30	DTT	natural abundance	2 mM

Sample #7

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-13C; U-15N] sN3(S235F), 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
31	sN3(S235F)	[U-13C; U-15N]	500 uM
32	sUbl1	natural abundance	550 uM
33	sodium phosphate	natural abundance	50 mM
34	sodium chloride	natural abundance	250 mM
35	DTT	natural abundance	2 mM

Release date

2021-12-29

Citation

The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a
Bessa, L.M., Guseva, S., Camacho-Zarco, A.R., Salvi, N., Maurin, D., Perez, L.M., Botova, M., Malki, A., Nanao, M., Jensen, M.R., Ruigrok, R., Blackledge, M.
Sci. Adv. (2022), 8, eabm4034-eabm4034, PubMed 35044811 , DOI 10.1126/sciadv.abm4034 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 51052 released on 2021-08-09
Title Assignment of nsp3a-nucleoprotein complex of SARS-CoV-2

Related entities 1. 3C-like proteinase (E.C.3.4.19.12,3.4.22.69), Nucleoprotein, entity 1, : 43 entities Detail

Related entities 2. 3C-like proteinase (E.C.3.4.19.12,3.4.22.69), Nucleoprotein, entity 2, : 6 entities Detail

Experiments performed 7 experiments Detail

1 NOESY

Instrument

Bruker AVANCE III HD - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
26	sN3	natural abundance	500 uM
27	sUbl1	natural abundance	550 uM
28	sodium phosphate	natural abundance	50 mM
29	sodium chloride	natural abundance	250 mM
30	DTT	natural abundance	2 mM

2 15N edited 3D NOESY-HSQC

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-15N] sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	sN3	[U-15N]	500 uM
2	sUbl1	natural abundance	550 uM
3	sodium phosphate	natural abundance	50 mM
4	sodium chloride	natural abundance	250 mM
5	DTT	natural abundance	2 mM

3 13C edited 3D NOESY-HSQC

Instrument

Bruker AVANCE III HD - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-13C; U-15N] sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	sN3	[U-13C; U-15N]	500 uM
7	sUbl1	natural abundance	550 uM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	250 mM
10	DTT	natural abundance	2 mM

4 13C edited 3D NOESY-HSQC

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-13C; U-15N] sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
16	sN3	natural abundance	550 uM
17	sUbl1	[U-13C; U-15N]	500 uM
18	sodium phosphate	natural abundance	50 mM
19	sodium chloride	natural abundance	250 mM
20	DTT	natural abundance	2 mM

5 13C edited NOESY-HSQC

Instrument

Bruker AVANCE III HD - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM 100% A220I Cd1 13C sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	sN3	natural abundance	550 uM
22	sUbl1	100% A220I Cd1 13C	500 uM
23	sodium phosphate	natural abundance	50 mM
24	sodium chloride	natural abundance	250 mM
25	DTT	natural abundance	2 mM

6 15N edited 3D NOESY-HSQC

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-15N] sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
11	sN3	natural abundance	550 uM
12	sUbl1	[U-15N]	500 uM
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	250 mM
15	DTT	natural abundance	2 mM

7 13C edited 3D NOESY-HSQC

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-13C; U-15N] sN3(S235F), 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
31	sN3(S235F)	[U-13C; U-15N]	500 uM
32	sUbl1	natural abundance	550 uM
33	sodium phosphate	natural abundance	50 mM
34	sodium chloride	natural abundance	250 mM
35	DTT	natural abundance	2 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34661_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: bmr34661_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1071		91.8 (chain: 2, length: 73), 97.9 (chain: 1, length: 96)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 73, Sequence coverage: 91.8%
  - Entity_assembly_ID: 1, Chain length: 96, Sequence coverage: 97.9%
- Total number of assignments
  - ¹H chemical shifts: 593
  - ¹³C chemical shifts: 322
  - ¹⁵N chemical shifts: 156
- Completeness of assignments
  - Entity_assemble_ID: 2
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- 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: 2
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	430	146	34.0
¹³C chemical shifts	293	111	37.9
¹⁵N chemical shifts	88	64	72.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	151	96	63.6
¹³C chemical shifts	146	47	32.2
¹⁵N chemical shifts	70	64	91.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	279	50	17.9
¹³C chemical shifts	147	64	43.5
¹⁵N chemical shifts	18	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	8	25.8
¹³C chemical shifts	31	8	25.8

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
33	THR	HG1	5.427

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	570	330	57.9
¹³C chemical shifts	446	211	47.3
¹⁵N chemical shifts	99	92	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	192	166	86.5
¹³C chemical shifts	192	74	38.5
¹⁵N chemical shifts	92	91	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	378	164	43.4
¹³C chemical shifts	254	137	53.9
¹⁵N chemical shifts	7	1	14.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	50	86.2
¹³C chemical shifts	58	50	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	0	0.0
¹³C chemical shifts	56	0	0.0
¹⁵N chemical shifts	1	1	100.0

Keywords SARS-Cov-2; nucleoprotein; nsp3; NMR; intrinsically disordered protein; chaperone; replication; nucleocapsid; RNA; SAXS, VIRAL PROTEIN

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 (0.65 seconds)

BMRB: 34661

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Sample #7

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. 3C-like proteinase (E.C.3.4.19.12,3.4.22.69), Nucleoprotein, entity 1, : 43 entities Detail

Related entities 2. 3C-like proteinase (E.C.3.4.19.12,3.4.22.69), Nucleoprotein, entity 2, : 6 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail