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- PDB-8ca6: Crystal structure of SARS-CoV-2 Mpro-Q189K mutant, free enzyme -

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Basic information

Entry
Database: PDB / ID: 8ca6
TitleCrystal structure of SARS-CoV-2 Mpro-Q189K mutant, free enzyme
ComponentsNon-structural protein 11
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 / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / endonuclease activity / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / methylation / 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 / host cell perinuclear region of cytoplasm / regulation of autophagy / 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: 1.92 Å
AuthorsEl Kilani, H. / 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 24, 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

Downloads & links

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Assembly

Deposited unit
AAA: Non-structural protein 11
BBB: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)67,6532
Polymers67,6532
Non-polymers00
Water1,31573
1
AAA: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)33,8271
Polymers33,8271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)33,8271
Polymers33,8271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.750, 106.633, 53.589
Angle α, β, γ (deg.)90.000, 104.725, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Non-structural protein 11 / nsp11


Mass: 33826.598 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium formate, 0.1M Bis-Tris propane pH6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.92→46.61 Å / Num. obs: 40519 / % possible obs: 98.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.5
Reflection shellResolution: 1.92→1.97 Å / Num. unique obs: 2697 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→46.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.475 / SU ML: 0.296 / Cross valid method: FREE R-VALUE / ESU R: 0.23 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2944 1966 4.855 %
Rwork0.2361 38528 -
all0.239 --
obs-40494 98.277 %
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: 47.455 Å2
Baniso -1Baniso -2Baniso -3
1-5.191 Å2-0 Å2-1.458 Å2
2---3.797 Å2-0 Å2
3----0.552 Å2
Refinement stepCycle: LAST / Resolution: 1.92→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 0 73 4769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134801
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154463
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.6396523
X-RAY DIFFRACTIONr_angle_other_deg1.2541.57610255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.315605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70723.151238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54915775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0031522
X-RAY DIFFRACTIONr_chiral_restr0.0650.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021140
X-RAY DIFFRACTIONr_nbd_refined0.2210.21055
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.24647
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22298
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22379
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2171
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1150.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.224
X-RAY DIFFRACTIONr_nbd_other0.240.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.27
X-RAY DIFFRACTIONr_mcbond_it4.1384.8672426
X-RAY DIFFRACTIONr_mcbond_other4.1384.8642425
X-RAY DIFFRACTIONr_mcangle_it6.0017.2893029
X-RAY DIFFRACTIONr_mcangle_other67.2923030
X-RAY DIFFRACTIONr_scbond_it4.1425.2532375
X-RAY DIFFRACTIONr_scbond_other4.1415.2552376
X-RAY DIFFRACTIONr_scangle_it6.2767.733494
X-RAY DIFFRACTIONr_scangle_other6.2757.7323495
X-RAY DIFFRACTIONr_lrange_it9.19858.5855266
X-RAY DIFFRACTIONr_lrange_other9.19858.5965263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.4481290.4382820X-RAY DIFFRACTION98.006
1.97-2.0240.4261280.4212728X-RAY DIFFRACTION97.0109
2.024-2.0820.4091420.3982690X-RAY DIFFRACTION98.2651
2.082-2.1460.3811430.3742652X-RAY DIFFRACTION99.1486
2.146-2.2170.3881310.3772543X-RAY DIFFRACTION98.8905
2.217-2.2940.3731140.3372468X-RAY DIFFRACTION98.8893
2.294-2.3810.3411440.3242369X-RAY DIFFRACTION99.0931
2.381-2.4780.3011310.3082291X-RAY DIFFRACTION99.1404
2.478-2.5880.3691050.2622205X-RAY DIFFRACTION98.7602
2.588-2.7140.3281000.2752100X-RAY DIFFRACTION98.39
2.714-2.860.367940.2451938X-RAY DIFFRACTION95.4439
2.86-3.0330.261990.2081849X-RAY DIFFRACTION96.5791
3.033-3.2420.339920.2021765X-RAY DIFFRACTION98.8818
3.242-3.50.2481010.2031651X-RAY DIFFRACTION98.5931
3.5-3.8330.248920.2021522X-RAY DIFFRACTION98.8365
3.833-4.2820.207510.1671411X-RAY DIFFRACTION99.2532
4.282-4.9390.225510.1691244X-RAY DIFFRACTION99.3098
4.939-6.0360.273550.206983X-RAY DIFFRACTION94.4495
6.036-8.4830.262410.19831X-RAY DIFFRACTION100
8.483-46.610.304230.179469X-RAY DIFFRACTION98.4

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