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Basic information

Entry
Database: PDB / ID: 7sna
TitleCrystallization of feline coronavirus Mpro with GC376 reveals mechanism of inhibition
Components3C-like proteinase
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / viral genome replication / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / 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 / endonuclease activity ...host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / viral genome replication / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / 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 / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus ...Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / 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 / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / 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 / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Papain-like protease, N-terminal domain superfamily, 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase
Similarity search - Domain/homology
Chem-UED / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesFeline coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKhan, M.B. / Lu, J. / Young, H.S. / Lemieux, M.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)VR3-172655 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)549297-2019 Canada
CitationJournal: Front Chem / Year: 2022
Title: Crystallization of Feline Coronavirus M pro With GC376 Reveals Mechanism of Inhibition.
Authors: Lu, J. / Chen, S.A. / Khan, M.B. / Brassard, R. / Arutyunova, E. / Lamer, T. / Vuong, W. / Fischer, C. / Young, H.S. / Vederas, J.C. / Lemieux, M.J.
History
DepositionOct 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0944
Polymers66,2832
Non-polymers8112
Water7,855436
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.660, 66.740, 79.070
Angle α, β, γ (deg.)90.000, 91.061, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-611-

HOH

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Components

#1: Protein 3C-like proteinase / Main Protease


Mass: 33141.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline coronavirus / Production host: Escherichia coli (E. coli) / References: UniProt: B0LJQ9
#2: Chemical ChemComp-UED / N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide / GC373 bound form, GC376 bound form


Mass: 405.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium chloride dihydrate, 0.1 M MES, 20% (w/v) PEG 6000, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→45.72 Å / Num. obs: 36262 / % possible obs: 99.74 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.94
Reflection shellResolution: 2.05→2.123 Å / Num. unique obs: 3598 / CC1/2: 0.755

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WTM

6wtm


Resolution: 2.05→45.72 Å / SU ML: 0.2645 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7667
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 1812 5 %
Rwork0.1736 34415 -
obs0.1763 36227 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.56 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4623 0 58 436 5117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01264777
X-RAY DIFFRACTIONf_angle_d1.226470
X-RAY DIFFRACTIONf_chiral_restr0.0592718
X-RAY DIFFRACTIONf_plane_restr0.0134835
X-RAY DIFFRACTIONf_dihedral_angle_d6.5884673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.37341370.30512615X-RAY DIFFRACTION99.28
2.11-2.170.3031390.25362637X-RAY DIFFRACTION99.89
2.17-2.240.31131380.21642630X-RAY DIFFRACTION99.6
2.24-2.320.27991400.21852642X-RAY DIFFRACTION99.71
2.32-2.410.27151380.20692634X-RAY DIFFRACTION99.82
2.41-2.520.28141370.18982598X-RAY DIFFRACTION99.78
2.52-2.650.24721410.17722669X-RAY DIFFRACTION99.65
2.65-2.820.21391390.17722638X-RAY DIFFRACTION99.75
2.82-3.040.24061390.17962653X-RAY DIFFRACTION99.93
3.04-3.340.2861390.17072631X-RAY DIFFRACTION99.89
3.34-3.830.21891410.15782675X-RAY DIFFRACTION99.96
3.83-4.820.15011400.13152665X-RAY DIFFRACTION99.89
4.82-45.720.18731440.16442728X-RAY DIFFRACTION99.72
Refinement TLS params.Method: refined / Origin x: 18.9943757232 Å / Origin y: 1.28141548162 Å / Origin z: 22.3862217941 Å
111213212223313233
T0.230301320977 Å20.00477410145026 Å2-0.00596678461956 Å2-0.232059144531 Å20.00732925650107 Å2--0.237129864757 Å2
L0.190646770881 °2-0.00532226133657 °2-0.0486247354207 °2-0.407361902254 °2-0.0129422126281 °2--0.773687808065 °2
S0.0135394291111 Å °0.0081173029112 Å °-0.0080321153771 Å °-0.00543508612887 Å °-0.0138050076116 Å °0.0154568746071 Å °0.0161060756436 Å °0.0308804030828 Å °-0.00185005732036 Å °
Refinement TLS groupSelection details: all

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