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- PDB-5utv: SARS-unique fold in the Rousettus Bat Coronavirus HKU9 -

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Basic information

Entry
Database: PDB / ID: 5utv
TitleSARS-unique fold in the Rousettus Bat Coronavirus HKU9
ComponentsPapain-like proteinase
KeywordsVIRAL PROTEIN / coronavirus / nonstructural protein 3 / HKU9 / SARS-unique domain
Function / homology
Function and homology information


: / RNA exonuclease activity / : / host cell membrane / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment ...: / RNA exonuclease activity / : / host cell membrane / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / membrane => GO:0016020 / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / zinc ion binding / ATP binding
Similarity search - Function
RNA-dependent RNA polymerase, bat coronavirus HKU9-like / Non-structural protein NSP3, SUD-C domain, bat CoV HKU9-like / Non-structural protein 2, bat coronavirus HKU9-like / Viral (Superfamily 1) RNA helicase / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...RNA-dependent RNA polymerase, bat coronavirus HKU9-like / Non-structural protein NSP3, SUD-C domain, bat CoV HKU9-like / Non-structural protein 2, bat coronavirus HKU9-like / Viral (Superfamily 1) RNA helicase / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / 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 (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / 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 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesRousettus bat coronavirus HKU9
MethodSOLUTION NMR / energy minimization
AuthorsHammond, R.G. / Tan, X. / Johnson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119456 United States
CitationJournal: Protein Sci. / Year: 2017
Title: SARS-unique fold in the Rousettus bat coronavirus HKU9.
Authors: Hammond, R.G. / Tan, X. / Johnson, M.A.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.title
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 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

Downloads & links

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Assembly

Deposited unit
A: Papain-like proteinase


Theoretical massNumber of molelcules
Total (without water)8,7361
Polymers8,7361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4800 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Papain-like proteinase / Non-structural protein 3


Mass: 8736.021 Da / Num. of mol.: 1 / Fragment: HKU9 NSP3 C domain, UNP residues 1345-1418
Source method: isolated from a genetically manipulated source
Details: synthetic gene (Genscript) / Source: (gene. exp.) Rousettus bat coronavirus HKU9 / Gene: rep, 1a-1b / Plasmid: pET-15bTEV_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0C6W5, 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-IDSample stateSpectrometer-IDType
111anisotropic13D CBCA(CO)NH
121anisotropic13D HNCO
131anisotropic13D HNCA
141anisotropic33D 1H-15N NOESY
151anisotropic33D 1H-13C NOESY aliphatic
171anisotropic33D 1H-13C NOESY aromatic
161anisotropic23D HBHA(CO)NH
192anisotropic23D 1H-15N TOCSY
181anisotropic13D C(CO)NH
1101anisotropic13D (H)CCH-COSY
1111anisotropic13D (H)CCH-TOCSY
1121anisotropic22D 1H-15N HSQC
1141anisotropic22D 1H-13C HSQC aliphatic
1151anisotropic22D 1H-13C HSQC aromatic
1161anisotropic13D HN(CA)CB
1171anisotropic12D (HB)CB(CGCD)HD
1181anisotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.2 mM [U-13C; U-15N] HKU9 NSP3 C domain, 5 mM [U-98% 2H] DTT, .02 % sodium azide, 97% H2O/3% D2O15N,13C_sample97% H2O/3% D2O
solution2637 uM [U-15N] HKU9 NSP3 C domain, 5 mM [U-98% 2H] DTT, .02 % sodium azide, 97% H2O/3% D2O15N_sample97% H2O/3% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMHKU9 NSP3 C domain[U-13C; U-15N]1
5 mMDTT[U-98% 2H]1
.02 %sodium azidenatural abundance1
637 uMHKU9 NSP3 C domain[U-15N]2
5 mMDTT[U-98% 2H]2
.02 %sodium azidenatural abundance2
Sample conditionsIonic strength: .253 M / Label: Conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III8503

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure calculation
Unio '102.0.3Serrano P, Pedrini B, Mohanty B, Geralt M, Herrmann T, Wuthrich K.peak picking
CARA1.9.0Keller and Wuthrichdata analysis
Analysis2.4CCPNdata analysis
TopSpin3.5Bruker Biospincollection
AmberAMBER03Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: energy minimization / Software ordinal: 7
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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