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- PDB-7skr: BtSCoV-Rf1.2004 Papain-Like protease bound to the non-covalent in... -

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Basic information

Entry
Database: PDB / ID: 7skr
TitleBtSCoV-Rf1.2004 Papain-Like protease bound to the non-covalent inhibitor 37
Components3C-like proteinase
KeywordsHYDROLASE/INHIBITOR / Papain-like Protease / VIRAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / viral genome replication / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / transferase activity / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / membrane => GO:0016020 ...host cell membrane / viral genome replication / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / transferase activity / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / identical protein binding
Similarity search - Function
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 / NSP1, C-terminal domain, betacoronavirus ...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 / NSP1, C-terminal domain, betacoronavirus / 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 / 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 / NSP1, globular domain, alpha/betacoronavirus / 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. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesBat SARS CoV Rf1/2004 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsDurie, I. / Shepard, J. / Freitas, B. / O'Boyle, B. / Enos, S. / Pegan, S.D.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI151006
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Exploring Noncovalent Protease Inhibitors for the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses.
Authors: Freitas, B.T. / Ahiadorme, D.A. / Bagul, R.S. / Durie, I.A. / Ghosh, S. / Hill, J. / Kramer, N.E. / Murray, J. / O'Boyle, B.M. / Onobun, E. / Pirrone, M.G. / Shepard, J.D. / Enos, S. / ...Authors: Freitas, B.T. / Ahiadorme, D.A. / Bagul, R.S. / Durie, I.A. / Ghosh, S. / Hill, J. / Kramer, N.E. / Murray, J. / O'Boyle, B.M. / Onobun, E. / Pirrone, M.G. / Shepard, J.D. / Enos, S. / Subedi, Y.P. / Upadhyaya, K. / Tripp, R.A. / Cummings, B.S. / Crich, D. / Pegan, S.D.
History
DepositionOct 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5005
Polymers35,8761
Non-polymers6244
Water45025
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,00010
Polymers71,7512
Non-polymers1,2498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-2/31
Buried area3360 Å2
ΔGint-59 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.306, 176.306, 79.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

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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: 35875.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat SARS CoV Rf1/2004 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q0QDZ2, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase
#2: Chemical ChemComp-9OZ / N-[(2-methoxypyridin-4-yl)methyl]-2-[(1R)-1-(naphthalen-1-yl)ethyl]-2-azaspiro[3.3]heptane-6-carboxamide


Mass: 415.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.99 Å3/Da / Density % sol: 75.36 % / Description: bipyramidal crystals
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl pH 8.5, 0.6M sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 16643 / % possible obs: 99.5 % / Redundancy: 13.7 % / CC1/2: 0.982 / CC star: 0.995 / Net I/σ(I): 15.5
Reflection shellResolution: 2.9→2.95 Å / Num. unique obs: 811 / CC1/2: 0.762 / CC star: 0.93 / Rpim(I) all: 0.273 / Χ2: 0.386

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E9S

3e9s


Resolution: 2.89→38.62 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 844 5.11 %
Rwork0.2009 15664 -
obs0.2028 16508 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.28 Å2 / Biso mean: 67.0875 Å2 / Biso min: 28.27 Å2
Refinement stepCycle: final / Resolution: 2.89→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 37 25 2540
Biso mean--89.61 60.83 -
Num. residues----313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-3.070.33541350.30272432256794
3.07-3.310.29981510.269525842735100
3.31-3.640.29571430.220426122755100
3.64-4.170.22941350.194826312766100
4.17-5.250.18841390.15972671281099
5.25-38.620.21951410.18812734287596

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