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- PDB-8c9p: Crystal structure of SARS-CoV-2 Mpro-E166V mutant, free enzyme -

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Basic information

Entry
Database: PDB / ID: 8c9p
TitleCrystal structure of SARS-CoV-2 Mpro-E166V mutant, free enzyme
Components3C-like proteinase nsp5
KeywordsANTIVIRAL PROTEIN / Mpro mutations main protease SARS-CoV-2
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / endonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
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 / Carbamoyl-phosphate synthase subdomain signature 2. ...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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / 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 / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto 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. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, 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 / Papain-like protease, thumb domain 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 replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEl Kilani, H. / Ibrahim, M. / Hilgenfeld, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: Crystals / Year: 2025
Title: 13b-K and Nirmatrelvir Resistance Mutations of SARS-CoV-2 Main Protease: Structural, Biochemical, and Biophysical Characterization of Free Enzymes and Inhibitor Complexes
Authors: El Kilani, H. / Sun, X. / Ibrahim, M.F. / Curth, U. / Hilgenfeld, R.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)33,6671
Polymers33,6671
Non-polymers00
Water81145
1
AAA: 3C-like proteinase nsp5

AAA: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)67,3352
Polymers67,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3060 Å2
ΔGint-15 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.594, 53.930, 44.754
Angle α, β, γ (deg.)90.000, 101.003, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-441-

HOH

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Components

#1: Protein 3C-like proteinase nsp5 / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33667.434 Da / Num. of mol.: 1 / Mutation: E166V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1MBis Tris Propane pH 6.50.2 MPotassium thiocyanate20 % w/vPEG 335010% v/vEthylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2→48.55 Å / Num. obs: 17883 / % possible obs: 98.77 % / Redundancy: 5 % / Biso Wilson estimate: 41.61 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 13.62
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.9355 / Num. unique obs: 1768 / CC1/2: 0.577 / % possible all: 98.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.55 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.606 / SU ML: 0.204 / Cross valid method: FREE R-VALUE / ESU R: 0.247 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.277 872 4.876 %
Rwork0.2126 17012 -
all0.216 --
obs-17883 98.779 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.789 Å2
Baniso -1Baniso -2Baniso -3
1-2.636 Å2-0 Å20.088 Å2
2---0.462 Å20 Å2
3----2.053 Å2
Refinement stepCycle: LAST / Resolution: 2→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 0 45 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132409
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152239
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6383275
X-RAY DIFFRACTIONr_angle_other_deg1.3491.5755141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3355304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27123.109119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66615385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3251511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
X-RAY DIFFRACTIONr_nbd_refined0.2210.2475
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22239
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0890.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.224
X-RAY DIFFRACTIONr_nbd_other0.2010.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.27
X-RAY DIFFRACTIONr_mcbond_it4.5075.0041219
X-RAY DIFFRACTIONr_mcbond_other4.4975.0021218
X-RAY DIFFRACTIONr_mcangle_it5.9237.51522
X-RAY DIFFRACTIONr_mcangle_other5.9217.5041523
X-RAY DIFFRACTIONr_scbond_it4.9055.3851190
X-RAY DIFFRACTIONr_scbond_other4.9035.3871191
X-RAY DIFFRACTIONr_scangle_it6.7577.911753
X-RAY DIFFRACTIONr_scangle_other6.7567.9121754
X-RAY DIFFRACTIONr_lrange_it8.63858.6272615
X-RAY DIFFRACTIONr_lrange_other8.63858.6092610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.32660.331228X-RAY DIFFRACTION98.5529
2.052-2.1080.353680.3181200X-RAY DIFFRACTION98.677
2.108-2.1690.331630.3171176X-RAY DIFFRACTION97.1765
2.169-2.2360.345670.2911155X-RAY DIFFRACTION99.7551
2.236-2.3090.336620.2621110X-RAY DIFFRACTION99.4907
2.309-2.390.383520.2661086X-RAY DIFFRACTION99.5626
2.39-2.480.304470.2361064X-RAY DIFFRACTION99.6413
2.48-2.5810.284490.2251012X-RAY DIFFRACTION99.2516
2.581-2.6950.334460.236987X-RAY DIFFRACTION99.2315
2.695-2.8270.308360.252926X-RAY DIFFRACTION97.8637
2.827-2.9790.372570.221864X-RAY DIFFRACTION98.3974
2.979-3.1590.282310.215810X-RAY DIFFRACTION96.1143
3.159-3.3770.244360.212785X-RAY DIFFRACTION99.8783
3.377-3.6460.278410.201742X-RAY DIFFRACTION100
3.646-3.9920.228400.195671X-RAY DIFFRACTION99.7195
3.992-4.4610.251260.164634X-RAY DIFFRACTION99.5475
4.461-5.1450.222270.181537X-RAY DIFFRACTION99.4709
5.145-6.2880.313270.214448X-RAY DIFFRACTION93.8735
6.288-8.8370.248220.183368X-RAY DIFFRACTION100
8.837-48.550.18890.151209X-RAY DIFFRACTION98.1982

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