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- PDB-7pku: Structure of SARS-CoV-2 nucleoprotein in dynamic complex with its... -

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Basic information

Entry
Database: PDB / ID: 7pku
TitleStructure of SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a
Components
  • 3C-like proteinase
  • Nucleoprotein
KeywordsVIRAL PROTEIN / SARS-Cov-2 / nucleoprotein / nsp3 / NMR / intrinsically disordered protein / chaperone / replication / nucleocapsid / RNA / SAXS
Function / homology
Function and homology information


host cell membrane / membrane => GO:0016020 / viral genome replication / transferase activity / viral nucleocapsid / SARS coronavirus main proteinase / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / membrane => GO:0016020 / viral genome replication / transferase activity / viral nucleocapsid / SARS coronavirus main proteinase / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / RNA binding / zinc ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #350 / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Ubiquitin-like (UB roll) ...Ubiquitin-like (UB roll) - #350 / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Ubiquitin-like (UB roll) / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / Coronavirus replicase NSP2, C-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Nucleoprotein / 3C-like proteinase
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLUTION NMR / simulated annealing
AuthorsBessa, L.M. / Guseva, S. / Camacho-Zarco, A.R. / Salvi, N. / Blackledge, M.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)SARS2NUCLEOPROTEINEuropean Union
European Research Council (ERC)DynamicAssembliesEuropean Union
CitationJournal: Sci Adv / Year: 2022
Title: The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a.
Authors: 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.W.H. / Blackledge, M.
History
DepositionAug 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)18,6042
Polymers18,6042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000target function
RepresentativeModel #1target function

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Components

#1: Protein 3C-like proteinase / Growth factor-like peptide / Leader protein / Non-structural protein 10 / Non-structural protein 2 ...Growth factor-like peptide / Leader protein / Non-structural protein 10 / Non-structural protein 2 / Non-structural protein 3 / Non-structural protein 4 / Non-structural protein 6 / Non-structural protein 7 / Non-structural protein 8 / Non-structural protein 9 / Papain-like proteinase / p65 homolog


Mass: 10893.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: ORF1ab / Production host: Escherichia coli (E. coli)
References: UniProt: A0A6M4N019, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase
#2: Protein Nucleoprotein


Mass: 7710.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: A0A6G9KDV1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
616isotropic2NOESY
121isotropic115N edited 3D NOESY-HSQC
363isotropic115N edited 3D NOESY-HSQC
232isotropic213C edited 3D NOESY-HSQC
444isotropic113C edited 3D NOESY-HSQC
555isotropic213C edited NOESY-HSQC
777isotropic113C edited 3D NOESY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM [U-15N] sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O1:1 complex15N sN3:U sUbl190% H2O/10% D2O
solution6500 uM sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O1:1 complexU sN3:U sUbl190% H2O/10% D2O
solution3500 uM [U-15N] sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O1:1 complex15N sUbl1:U sN390% H2O/10% D2O
solution2500 uM [U-13C; U-15N] sN3, 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O1:1 complex13C, 15N sN3:U sUbl190% H2O/10% D2O
solution7500 uM [U-13C; U-15N] sN3(S235F), 550 uM sUbl1, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O1:1 complex S235F mutant of N313C, 15N sN3 (S235F):U sUbl190% H2O/10% D2O
solution4500 uM [U-13C; U-15N] sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O1:1 complex13C, 15N sUbl1:U sN390% H2O/10% D2O
solution5500 uM 100% A220I Cd1 13C sUbl1, 550 uM sN3, 50 mM sodium phosphate, 250 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O1:1 complex, specific labelling of A220I Cdelta113C, sUbl1:U sN390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMsN3[U-15N]1
550 uMsUbl1natural abundance1
50 mMsodium phosphatenatural abundance1
250 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
500 uMsN3natural abundance6
550 uMsUbl1natural abundance6
50 mMsodium phosphatenatural abundance6
250 mMsodium chloridenatural abundance6
2 mMDTTnatural abundance6
500 uMsUbl1[U-15N]3
550 uMsN3natural abundance3
50 mMsodium phosphatenatural abundance3
250 mMsodium chloridenatural abundance3
2 mMDTTnatural abundance3
500 uMsN3[U-13C; U-15N]2
550 uMsUbl1natural abundance2
50 mMsodium phosphatenatural abundance2
250 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
500 uMsN3(S235F)[U-13C; U-15N]7
550 uMsUbl1natural abundance7
50 mMsodium phosphatenatural abundance7
250 mMsodium chloridenatural abundance7
2 mMDTTnatural abundance7
500 uMsUbl1[U-13C; U-15N]4
550 uMsN3natural abundance4
50 mMsodium phosphatenatural abundance4
250 mMsodium chloridenatural abundance4
2 mMDTTnatural abundance4
500 uMsUbl1100% A220I Cd1 13C5
550 uMsN3natural abundance5
50 mMsodium phosphatenatural abundance5
250 mMsodium chloridenatural abundance5
2 mMDTTnatural abundance5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1250 mM16.51 atm298 K
2250 mM16.51 atm298 K
3250 mM16.51 atm298 K
4250 mM16.51 atm298 K
5250 mM16.51 atm298 K
6250 mM16.51 atm298 K
7250 mM16.51 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9501
Bruker AVANCE III HDBrukerAVANCE III HD8502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRFAM-SPARKYLee, W., Tonelli, M., and Markley, J.L.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 10

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