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- PDB-2jzd: NMR structure of the domain 527-651 of the SARS-CoV nonstructural... -

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Entry
Database: PDB / ID: 2jzd
TitleNMR structure of the domain 527-651 of the SARS-CoV nonstructural protein nsp3
ComponentsReplicase polyprotein 1ab
KeywordsVIRAL PROTEIN / SARS-CoV / SARS-unique domain / nonstructural protein / nsp3 / nsp3c / Functional and Structural Proteomics of SARS-CoV-Related Proteins / FSPS / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / ATP-binding / Cytoplasm / Endonuclease / Exonuclease / Helicase / Hydrolase / Membrane / Metal-binding / Nuclease / Nucleotide-binding / Nucleotidyltransferase / Protease / Ribosomal frameshift / RNA replication / RNA-binding / RNA-directed RNA polymerase / Thiol protease / Transferase / Transmembrane / Zinc / Zinc-finger
Function / homology
Function and homology information


viral RNA-directed RNA polymerase complex / viral replication complex formation and maintenance / exoribonuclease complex / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : ...viral RNA-directed RNA polymerase complex / viral replication complex formation and maintenance / exoribonuclease complex / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : / : / endopeptidase complex / endoribonuclease complex / mRNA capping enzyme complex / positive stranded viral RNA replication / suppression by virus of host type I interferon production / positive regulation of RNA biosynthetic process / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K48-linked deubiquitination / Translation of Replicase and Assembly of the Replication Transcription Complex / protein K63-linked deubiquitination / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / RNA-templated transcription / SARS-CoV-1 modulates host translation machinery / viral transcription / protein autoprocessing / 7-methylguanosine mRNA capping / positive regulation of viral genome replication / membrane => GO:0016020 / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / protein processing / symbiont-mediated suppression of host gene expression / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / protein dimerization activity / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane
Similarity search - Function
Nsp3, SUD-M subdomain / Leucine Aminopeptidase, subunit E; domain 1 / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus ...Nsp3, SUD-M subdomain / Leucine Aminopeptidase, subunit E; domain 1 / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / 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 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 single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSARS coronavirus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChatterjee, A. / Johnson, M.A. / Serrano, P. / Pedrini, B. / Joseph, J. / Saikatendu, K. / Neuman, B. / Stevens, R.C. / Wilson, I.A. / Buchmeier, M.J. ...Chatterjee, A. / Johnson, M.A. / Serrano, P. / Pedrini, B. / Joseph, J. / Saikatendu, K. / Neuman, B. / Stevens, R.C. / Wilson, I.A. / Buchmeier, M.J. / Kuhn, P. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: J.Virol. / Year: 2009
Title: Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold.
Authors: Chatterjee, A. / Johnson, M.A. / Serrano, P. / Pedrini, B. / Joseph, J.S. / Neuman, B.W. / Saikatendu, K. / Buchmeier, M.J. / Kuhn, P. / Wuthrich, K.
History
DepositionJan 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replicase polyprotein 1ab


Theoretical massNumber of molelcules
Total (without water)14,3671
Polymers14,3671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80target function
RepresentativeModel #6closest to the average

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Components

#1: Protein Replicase polyprotein 1ab / pp1ab / ORF1ab polyprotein [includes: Replicase polyprotein 1a / Non-structural proteins 1 / 2 / 3 ...pp1ab / ORF1ab polyprotein [includes: Replicase polyprotein 1a / Non-structural proteins 1 / 2 / 3 / 4 / 3C-like proteinase / Non-structural proteins 6 / 7 / 8 / 9 / 10 / RNA-directed RNA polymerase / Helicase / Exoribonuclease / Uridylate-specific endoribonuclease / Putative 2'-O-methyl transferase]


Mass: 14366.678 Da / Num. of mol.: 1
Fragment: Non-structural protein 3 (Domain 527-651): Residues 1345-1469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Gene: rep, 1a-1b / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P59641, UniProt: P0C6X7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D (H)CCH-TOCSY
1413D 1H-15N TOCSY
1513D 1H-13C NOESY aliphatic region
1613D 1H-13C NOESY aromatic region
1713D 1H-15N NOESY
1814D APSY-HN(CO)CA
1914D APSY-HACANH
11015D APSY-CBCA(CO)NH
11115D APSY-(HA)CA(CO)NH

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Sample preparation

DetailsContents: 1.4 mM [U-99% 13C; U-98% 15N] nsp3(527-651), 25 mM sodium phosphate, 150 mM sodium chloride, 2 mM sodium azide, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMnsp3(527-651)[U-99% 13C; U-98% 15N]1
25 mMsodium phosphate1
150 mMsodium chloride1
2 mMsodium azide1
10 %D2O1
Sample conditionsIonic strength: 0.227 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker DRXBrukerDRX7003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
CARA1.4Keller and Wuthrichdata analysis
CARA1.4Keller and Wuthrichchemical shift assignment
CARA1.4Keller and Wuthrichpeak picking
CYANA1.2Guntert, Mumenthaler and Wuthrichcreating chemical shift list
CYANA1.2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA1.2Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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