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- PDB-2m0a: Solution structure of MHV nsp3a -

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Basic information

Entry
Database: PDB / ID: 2m0a
TitleSolution structure of MHV nsp3a
ComponentsNon-structural protein 3
KeywordsHYDROLASE
Function / homology
Function and homology information


cysteine-type deubiquitinase activity => GO:0004843 / cytoplasmic viral factory / self proteolysis / host cell membrane / viral genome replication / SARS coronavirus main proteinase / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification ...cysteine-type deubiquitinase activity => GO:0004843 / cytoplasmic viral factory / self proteolysis / host cell membrane / viral genome replication / SARS coronavirus main proteinase / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / zinc ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #350 / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / Ubiquitin-like (UB roll) / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus ...Ubiquitin-like (UB roll) - #350 / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / Ubiquitin-like (UB roll) / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Replicase polyprotein 1a
Similarity search - Component
Biological speciesMurine hepatitis virus
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKeane, S.C. / Giedroc, D.P.
CitationJournal: J.Virol. / Year: 2013
Title: Solution Structure of Mouse Hepatitis Virus (MHV) nsp3a and Determinants of the Interaction with MHV Nucleocapsid (N) Protein.
Authors: Keane, S.C. / Giedroc, D.P.
History
DepositionOct 23, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 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

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Assembly

Deposited unit
A: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)12,6381
Polymers12,6381
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)21 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Non-structural protein 3 / nsp3 / PL1-PRO/PL2-PRO / PL1/PL2 / Papain-like proteinases 1/2 / p210


Mass: 12638.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine hepatitis virus / Strain: A59 / Gene: 1a / Production host: Escherichia coli (E. coli)
References: UniProt: P0C6V0, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D C(CO)NH
1613D H(CCO)NH
1723D (H)CCH-TOCSY
1823D (H)CCH-COSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11122D 1H-13C HSQC aliphatic
11222D 1H-13C HSQC aromatic
11313D HNHA
1141IPAP-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM potassium phosphate, 100 mM potassium chloride, 5 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
250 mM potassium phosphate, 100 mM potassium chloride, 5 mM TCEP, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMpotassium phosphate-11
100 mMpotassium chloride-21
5 mMTCEP-31
50 mMpotassium phosphate-42
100 mMpotassium chloride-52
5 mMTCEP-62
Sample conditionsIonic strength: 150 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
ProcheckNMRLaskowski and MacArthurdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: DGSA-distance geometry simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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