BMRB Entry 34661

Name: Structure of SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a
Published: 2022-01-16

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PDB ID: 7pku
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34661
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2021-08-26

Original release date:

2022-01-16

Authors:

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

Citation:

Citation: Bessa, Luiza Mamigonian; Guseva, Serafima; Camacho-Zarco, Aldo; Salvi, Nicola; Maurin, Damien; Perez, Laura Marino; Botova, Maiia; Malki, Anas; Nanao, Max; Jensen, Malene Ringkjobing; Ruigrok, Rob; Blackledge, Martin. "The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a" Sci. Adv. 8, eabm4034-eabm4034 (2022).
PubMed: 35044811

Assembly members:

Assembly members:
entity_1, polymer, 96 residues, 10893.183 Da.
entity_2, polymer, 73 residues, 7710.649 Da.

Natural source:

Natural source: Common Name: 2019-nCoV, SARS-CoV-2 Taxonomy ID: 2697049 Superkingdom: Viruses Kingdom: not available Genus/species: Betacoronavirus HCoV-SARS

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: QGYKSVNITFELDERIDKVL NEKCSAYTVELGTEVNEFAC VVADAVIKTLQPVSELLTPL GIDLDEWSMATYYLFDESGE FKLASHMYCSFYPPDE
entity_2: RNSSRNSTPGSSRGTSPARM AGNGGDAALALLLLDRLNQL ESKMSGKGQQQQGQTVTKKS AAEASKKPRQKRT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	322
15N chemical shifts	156
1H chemical shifts	593

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 96 residues - 10893.183 Da.

1

GLN

GLY

TYR

LYS

SER

VAL

ASN

ILE

THR

PHE

2

GLU

LEU

ASP

GLU

ARG

ILE

ASP

LYS

VAL

LEU

3

ASN

GLU

LYS

CYS

SER

ALA

TYR

THR

VAL

GLU

4

LEU

GLY

THR

GLU

VAL

ASN

GLU

PHE

ALA

CYS

5

VAL

ALA

ASP

ALA

VAL

ILE

LYS

THR

LEU

6

GLN

PRO

VAL

SER

GLU

LEU

THR

PRO

LEU

7

GLY

ILE

ASP

LEU

ASP

GLU

TRP

SER

MET

ALA

8

THR

TYR

LEU

PHE

ASP

GLU

SER

GLY

GLU

9

PHE

LYS

LEU

ALA

SER

HIS

MET

TYR

CYS

SER

10

PHE

TYR

PRO

ASP

GLU

Entity 2, unit_2 73 residues - 7710.649 Da.

1

ARG

ASN

SER

ARG

ASN

SER

THR

PRO

GLY

2

SER

ARG

GLY

THR

SER

PRO

ALA

ARG

MET

3

ALA

GLY

ASN

GLY

ASP

ALA

LEU

ALA

4

LEU

ASP

ARG

LEU

ASN

GLN

LEU

5

GLU

SER

LYS

MET

SER

GLY

LYS

GLY

GLN

6

GLN

GLY

GLN

THR

VAL

THR

LYS

SER

7

ALA

GLU

ALA

SER

LYS

PRO

ARG

GLN

8

LYS

ARG

THR

Samples:

sample_1: sN3, [U-15N], 500 uM; sUbl1 550 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM

sample_2: sN3, [U-13C; U-15N], 500 uM; sUbl1 550 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM

sample_3: sN3 550 uM; sUbl1, [U-15N], 500 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM

sample_4: sN3 550 uM; sUbl1, [U-13C; U-15N], 500 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM

sample_5: sN3 550 uM; sUbl1, 100% A220I Cd1 13C, 500 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM

sample_6: sN3 500 uM; sUbl1 550 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM

sample_7: sN3(S235F), [U-13C; U-15N], 500 uM; sUbl1 550 uM; sodium phosphate 50 mM; sodium chloride 250 mM; DTT 2 mM

sample_conditions_1: ionic strength: 250 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 250 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 250 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_4: ionic strength: 250 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_5: ionic strength: 250 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_6: ionic strength: 250 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_7: ionic strength: 250 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
NOESY	sample_6	isotropic	sample_conditions_6
15N edited 3D NOESY-HSQC	sample_1	isotropic	sample_conditions_1
13C edited 3D NOESY-HSQC	sample_2	isotropic	sample_conditions_2
13C edited 3D NOESY-HSQC	sample_4	isotropic	sample_conditions_4
13C edited NOESY-HSQC	sample_5	isotropic	sample_conditions_5
15N edited 3D NOESY-HSQC	sample_3	isotropic	sample_conditions_3
13C edited 3D NOESY-HSQC	sample_7	isotropic	sample_conditions_7

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMRFAM-SPARKY, Lee, W., Tonelli, M., and Markley, J.L. - data analysis

NMR spectrometers:

Bruker AVANCE III HD 950 MHz
Bruker AVANCE III HD 850 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks