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- PDB-9pfh: Crystal structure of SARS-CoV-2 Mpro Mutant P132H with C5a -

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Entry
Database: PDB / ID: 9pfh
TitleCrystal structure of SARS-CoV-2 Mpro Mutant P132H with C5a
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / HYDROLASE / Mutant / Inhibitor
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / regulation of autophagy / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / endonuclease activity / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome ...viral genome replication / methyltransferase activity / regulation of autophagy / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / endonuclease activity / 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 / methylation / 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 / 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 / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / viral translational frameshifting / 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
Coronavirus replicase NSP2, C-terminal / 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 ...Coronavirus replicase NSP2, C-terminal / 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 / Betacoronavirus single-stranded poly(A) binding domain / 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 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus replicase NSP2, N-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 Nsp3 ectodomain (3Ecto) 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
Chem-WZK / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKenward, C. / Mosimann, W.A. / Worrall, L.J. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Infect.Dis. / Year: 2025
Title: Functional and Structural Characterization of Treatment-Emergent Nirmatrelvir Resistance Mutations at Low Frequencies in the Main Protease (Mpro) Reveals a Unique Evolutionary Route for SARS- ...Title: Functional and Structural Characterization of Treatment-Emergent Nirmatrelvir Resistance Mutations at Low Frequencies in the Main Protease (Mpro) Reveals a Unique Evolutionary Route for SARS-CoV-2 to Gain Resistance.
Authors: Deschenes, N.M. / Perez-Vargas, J. / Zhong, Z. / Thomas, M. / Kenward, C. / Mosimann, W.A. / Worrall, L.J. / Waglechner, N. / Li, A.X. / Maguire, F. / Aftanas, P. / Smith, J.R. / Lim, J. / ...Authors: Deschenes, N.M. / Perez-Vargas, J. / Zhong, Z. / Thomas, M. / Kenward, C. / Mosimann, W.A. / Worrall, L.J. / Waglechner, N. / Li, A.X. / Maguire, F. / Aftanas, P. / Smith, J.R. / Lim, J. / Young, R.N. / Cherkasov, A. / Farooqi, L. / Moinuddin, A. / Siddiqi, L. / Malik, I. / Lefebvre, M. / Paetzel, M. / Strynadka, N.C.J. / Jean, F. / McGeer, A. / Kozak, R.A.
History
DepositionJul 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase nsp5
B: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6374
Polymers67,7332
Non-polymers9042
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-14 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.537, 98.678, 102.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 33866.578 Da / Num. of mol.: 2 / Fragment: UNP residues 3264-3569
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: Chemical ChemComp-WZK / N-[(4-chlorothiophen-2-yl)methyl]-N-[4-(dimethylamino)phenyl]-2-(5-hydroxyisoquinolin-4-yl)acetamide


Mass: 451.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22ClN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris, pH 8, 15% PEG8000, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1807 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1807 Å / Relative weight: 1
ReflectionResolution: 2.69→49.34 Å / Num. obs: 11182 / % possible obs: 92.5 % / Redundancy: 6.4 % / CC1/2: 0.962 / Rmerge(I) obs: 0.071 / Net I/σ(I): 5.5
Reflection shellResolution: 2.69→2.83 Å / Rmerge(I) obs: 1.09 / Num. unique obs: 80 / CC1/2: 0.648

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→49.34 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2831 1103 9.86 %
Rwork0.2226 --
obs0.2287 11181 56.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4665 0 62 10 4737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034854
X-RAY DIFFRACTIONf_angle_d0.7446604
X-RAY DIFFRACTIONf_dihedral_angle_d5.686672
X-RAY DIFFRACTIONf_chiral_restr0.042736
X-RAY DIFFRACTIONf_plane_restr0.006861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.810.388960.318562X-RAY DIFFRACTION3
2.81-2.960.6122150.2999202X-RAY DIFFRACTION9
2.96-3.140.3607380.2942410X-RAY DIFFRACTION18
3.14-3.380.34281030.2888909X-RAY DIFFRACTION41
3.38-3.720.31571840.25571737X-RAY DIFFRACTION79
3.72-4.260.28452450.21972183X-RAY DIFFRACTION99
4.26-5.370.27422490.19712232X-RAY DIFFRACTION100
5.37-49.340.24462630.20782343X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2296-0.3456-1.09451.66390.01622.331-0.3687-0.0743-0.2828-0.36970.2727-0.1493-0.2718-0.2168-0.35780.1607-0.0347-0.0680.36760.0063-0.1543-18.454-6.7717.881
21.1227-0.4379-1.13411.18210.16983.6137-0.0130.39950.0225-0.38260.18680.234-0.4528-1.04250.12790.2923-0.09440.00540.6434-0.07470.471-31.633-7.38122.005
31.1366-0.14821.12261.257-0.77632.9880.1419-0.25060.37610.15640.18830.28690.8201-0.557-0.1315-0.11410.17690.056-0.0135-0.03960.1855-12.379-5.87824.869
40.0317-0.06440.17580.1724-0.44641.0962-0.2372-0.6870.132-0.12910.1598-0.00470.24380.3782-0.0874-0.12290.0888-0.00670.3520.04840.4325-4.415-3.30933.808
51.3648-0.0901-0.98380.1021-0.17961.47760.3013-0.3122-0.7926-0.04-0.0085-0.10860.18280.98620.27640.0684-0.0668-0.13140.6157-0.01860.393517.601-6.58236.582
62.2146-0.46560.47312.88460.58942.03690.4794-0.159-0.64030.2699-0.2773-0.32970.2821-0.1780.03710.1853-0.00440.13970.32440.12030.413211.633-9.1936.852
71.8034-0.69150.4192.30710.50542.4609-0.48930.23610.2258-0.40380.20040.5604-0.20680.56250.14040.17530.039-0.0370.34840.05910.32978.761-4.14525.177
82.14250.0522-0.94240.8419-0.37991.3826-0.3248-0.1573-0.65860.16210.1502-0.06430.820.34650.03450.36610.0931-0.03020.2424-0.0770.3908-0.13-10.9671.311
93.38820.2131-1.40352.26070.54353.34430.1512-0.414-1.1259-0.5780.0712-0.43321.14751.07140.26330.80740.1784-0.06580.40610.00750.574.921-17.4-9.652
101.71640.96990.22591.5964-0.62843.8753-0.07360.2579-0.259-0.3471-0.06190.1430.49150.08150.14240.17390.02210.05120.3418-0.05440.30074.093-3.0793.695
111.61150.86460.86771.62080.21372.8475-0.24850.2706-0.45020.36630.12750.54290.10860.5842-0.27770.2461-0.11370.0030.25880.13450.545910.5886.4797.685
121.6066-0.36780.4682.42050.02120.653-0.11630.04770.4695-0.3662-0.0550.2789-0.33430.12110.19090.6197-0.18080.09910.5543-0.07370.42225.45925.17919.378
133.7432-0.3841-1.86362.0643-0.79775.2640.259-0.6480.1908-0.16220.44630.8329-1.53260.5570.51360.7388-0.0558-0.02840.4955-0.08690.60324.81821.92113.819
141.44761.1286-1.00572.69590.45094.00290.66120.7107-0.11060.8011-0.38540.25490.6020.60120.17240.5390.05570.15580.4634-0.04570.66-1.2949.80517.302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:43 )A1 - 43
2X-RAY DIFFRACTION2( CHAIN A AND RESID 44:100 )A44 - 100
3X-RAY DIFFRACTION3( CHAIN A AND RESID 101:180 )A101 - 180
4X-RAY DIFFRACTION4( CHAIN A AND RESID 181:213 )A181 - 213
5X-RAY DIFFRACTION5( CHAIN A AND RESID 214:234 )A214 - 234
6X-RAY DIFFRACTION6( CHAIN A AND RESID 235:274 )A235 - 274
7X-RAY DIFFRACTION7( CHAIN A AND RESID 275:300 )A275 - 300
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1:43 )B1 - 43
9X-RAY DIFFRACTION9( CHAIN B AND RESID 44:100 )B44 - 100
10X-RAY DIFFRACTION10( CHAIN B AND RESID 101:180 )B101 - 180
11X-RAY DIFFRACTION11( CHAIN B AND RESID 181:213 )B181 - 213
12X-RAY DIFFRACTION12( CHAIN B AND RESID 214:234 )B214 - 234
13X-RAY DIFFRACTION13( CHAIN B AND RESID 235:274 )B235 - 274
14X-RAY DIFFRACTION14( CHAIN B AND RESID 275:306 )B275 - 306

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