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Found 1 Document (0.795 seconds)

BMRB: 34511

8FD5

The N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein

Authors

Veverka, V., Boura, E.

Assembly

N-NTD

Entity

1. N-NTD (polymer, Thiol state: not present), 140 monomers, 15111.70 Da Detail

GAMGLPNNTA SWFTALTQHG KEDLKFPRGQ GVPINTNSSP DDQIGYYRRA TRRIRGGDGK MKDLSPRWYF YYLGTGPEAG LPYGANKDGI IWVATEGALN TPKDHIGTRN PANNAAIVLQ LPQGTTLPKG FYAEGSRGGS

Formula weight

15111.7 Da

Source organism

Severe acute respiratory syndrome coronavirus 2

Exptl. method

solution NMR

Refine. method

torsion angle dynamicsmolecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.3 %, Completeness (bb): 98.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (1518 of 1577)	97.2 % (800 of 823)	94.7 % (576 of 608)	97.3 % (142 of 146)
Backbone	98.5 % (806 of 818)	98.3 % (285 of 290)	98.7 % (394 of 399)	98.4 % (127 of 129)
Sidechain	94.4 % (829 of 878)	96.6 % (515 of 533)	91.2 % (299 of 328)	88.2 % (15 of 17)
Aromatic	77.1 % (108 of 140)	92.9 % (65 of 70)	59.7 % (40 of 67)	100.0 % (3 of 3)
Methyl	98.4 % (124 of 126)	96.8 % (61 of 63)	100.0 % (63 of 63)

1. entity 1

GAMGLPNNTA SWFTALTQHG KEDLKFPRGQ GVPINTNSSP DDQIGYYRRA TRRIRGGDGK MKDLSPRWYF YYLGTGPEAG LPYGANKDGI IWVATEGALN TPKDHIGTRN PANNAAIVLQ LPQGTTLPKG FYAEGSRGGS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM [U-13C; U-15N] N-NTD, 25 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

Protein Blocks Logo

Calculated from 40 models in PDB: 6YI3, Strand ID: A Detail

Release date

2020-04-01

Citation

Docking study of chloroquine and hydroxychloroquine interaction with RNA binding domain of nucleocapsid phospho-protein - an in silico insight into the comparative efficacy of repurposing antiviral drugs
Dinesh, D.C., Chalupska, D., Silhan, J., Koutna, E., Nencka, R., Veverka, V., Boura, E.
J. Biomol. Struct. Dyn. (2020), 16, 1-13, PubMed 32469265 , DOI 10.1080/07391102.2020.1775703 , Abstract

Related entities 1. N-NTD, : 1 : 3 : 23 : 69 entities Detail

Interaction partners 1. N-NTD, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 mM [U-13C; U-15N] N-NTD, 25 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

3 3D HNCO

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

4 3D HNCACB

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

5 3D CBCA(CO)NH

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

6 3D 1H-15N NOESY

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

7 3D 1H-13C NOESY

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

8 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	N-NTD	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	50 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34511_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: bmr34511_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1665		100.0 (chain: 1, length: 140)
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: 1, Chain length: 140, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 940
  - ¹³C chemical shifts: 574
  - ¹⁵N chemical shifts: 151
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
14	THR	HG1	6.337
38	SER	HG	5.492
72	TYR	HH	10.702
101	THR	HG1	5.777
125	THR	HG1	5.792

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	823	805	97.8
¹³C chemical shifts	608	574	94.4
¹⁵N chemical shifts	155	151	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	290	287	99.0
¹³C chemical shifts	280	277	98.9
¹⁵N chemical shifts	129	127	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	533	518	97.2
¹³C chemical shifts	328	297	90.5
¹⁵N chemical shifts	26	24	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	65	100.0
¹³C chemical shifts	65	65	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	63	90.0
¹³C chemical shifts	67	38	56.7
¹⁵N chemical shifts	3	3	100.0

Keywords COVID-19, MERS, RNA-binding domain, SARS, VIRAL PROTEIN

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Found 1 Document (0.795 seconds)

BMRB: 34511

Sample

Related entities 1. N-NTD, : 1 : 3 : 23 : 69 entities Detail

Interaction partners 1. N-NTD, : 3 interactors Detail

Experiments performed 8 experiments Detail

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Chemical shift validation 3 contents Detail