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- PDB-8c9l: Crystal structure of SARS-CoV-2 Mpro-S144A mutant, free enzyme -

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Basic information

Entry
Database: PDB / ID: 8c9l
TitleCrystal structure of SARS-CoV-2 Mpro-S144A 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 / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / endonuclease activity / 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 / omega peptidase activity / methylation / 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 / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell nucleus / 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: 1.7 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 1.0Feb 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: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)33,3341
Polymers33,3341
Non-polymers00
Water1,802100
1
AAA: 3C-like proteinase nsp5

AAA: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)66,6682
Polymers66,6682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2690 Å2
ΔGint-13 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.074, 53.694, 44.707
Angle α, β, γ (deg.)90.000, 102.049, 90.000
Int Tables number5
Space group name H-MC121

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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: 33334.016 Da / Num. of mol.: 1
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.: 100 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1MBis Tris Propane pH 6.50.02 MSodium potassium phosphate pH 7.520 % 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: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→48.38 Å / Num. obs: 28802 / % possible obs: 98.59 % / Redundancy: 5 % / Biso Wilson estimate: 35.01 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 16.97
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 2771 / CC1/2: 0.55 / CC star: 0.84 / % possible all: 96.28

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6y2e

6y2e


Resolution: 1.7→48.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.567 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.244 1428 4.955 %
Rwork0.2069 27394 -
all0.209 --
obs-28798 98.604 %
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: 37.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.893 Å20 Å20.658 Å2
2---1.056 Å2-0 Å2
3----0.108 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 0 100 2432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132384
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152213
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6393240
X-RAY DIFFRACTIONr_angle_other_deg1.3971.5755083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6595301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51323.193119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4961511
X-RAY DIFFRACTIONr_chiral_restr0.080.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
X-RAY DIFFRACTIONr_nbd_refined0.2060.2427
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22131
X-RAY DIFFRACTIONr_nbtor_refined0.170.21175
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2108
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.216
X-RAY DIFFRACTIONr_nbd_other0.1980.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0840.25
X-RAY DIFFRACTIONr_mcbond_it3.133.8171207
X-RAY DIFFRACTIONr_mcbond_other3.1223.8131205
X-RAY DIFFRACTIONr_mcangle_it4.1175.7191507
X-RAY DIFFRACTIONr_mcangle_other4.1155.721507
X-RAY DIFFRACTIONr_scbond_it3.9074.2041177
X-RAY DIFFRACTIONr_scbond_other3.9054.2061178
X-RAY DIFFRACTIONr_scangle_it5.5096.1441733
X-RAY DIFFRACTIONr_scangle_other5.5096.1461734
X-RAY DIFFRACTIONr_lrange_it7.10345.1232577
X-RAY DIFFRACTIONr_lrange_other7.09545.0772569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3311180.3271934X-RAY DIFFRACTION95.1762
1.744-1.7920.315920.2911988X-RAY DIFFRACTION99.0005
1.792-1.8430.2941020.2831909X-RAY DIFFRACTION99.2107
1.843-1.90.315840.271861X-RAY DIFFRACTION99.2347
1.9-1.9620.311010.2571800X-RAY DIFFRACTION99.4247
1.962-2.0310.316980.2421736X-RAY DIFFRACTION98.4962
2.031-2.1080.278870.2361689X-RAY DIFFRACTION98.6119
2.108-2.1940.285860.2381578X-RAY DIFFRACTION96.9132
2.194-2.2910.288650.221563X-RAY DIFFRACTION99.6938
2.291-2.4030.265740.2211538X-RAY DIFFRACTION99.6292
2.403-2.5320.344810.2281417X-RAY DIFFRACTION99.6673
2.532-2.6860.297650.231355X-RAY DIFFRACTION99.2313
2.686-2.8710.291620.2251255X-RAY DIFFRACTION99.1717
2.871-3.10.315630.2211136X-RAY DIFFRACTION95.7668
3.1-3.3950.219610.2061102X-RAY DIFFRACTION99.6572
3.395-3.7940.212520.1921001X-RAY DIFFRACTION99.5274
3.794-4.3770.165450.165879X-RAY DIFFRACTION99.8919
4.377-5.3530.203450.167747X-RAY DIFFRACTION99.3727
5.353-7.5350.202320.189562X-RAY DIFFRACTION95.9612
7.535-48.380.237150.15344X-RAY DIFFRACTION98.8981

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