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- PDB-8dz9: Crystal Structure of SARS-CoV-2 Main protease G143S mutant in com... -

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Basic information

Entry
Database: PDB / ID: 8dz9
TitleCrystal Structure of SARS-CoV-2 Main protease G143S mutant in complex with Nirmatrelvir
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Mpro / 3cl / covid / sars-cov-2 ensitrelvir / nirmatrelvir / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 toll-like receptor signaling pathway / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / 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 / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / 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 / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / 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 / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 / Trypsin-like serine proteases / 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. / : / :
Similarity search - Domain/homology
Chem-4WI / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.664 Å
AuthorsNoske, G.D. / Oliva, G. / Godoy, A.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/07600-3 Brazil
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.
Authors: Noske, G.D. / de Souza Silva, E. / de Godoy, M.O. / Dolci, I. / Fernandes, R.S. / Guido, R.V.C. / Sjo, P. / Oliva, G. / Godoy, A.S.
History
DepositionAug 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jul 26, 2023Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,5079
Polymers135,4224
Non-polymers2,0845
Water11,512639
1
A: 3C-like proteinase nsp5
B: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7925
Polymers67,7112
Non-polymers1,0813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-8 kcal/mol
Surface area25180 Å2
MethodPISA
2
C: 3C-like proteinase nsp5
D: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7144
Polymers67,7112
Non-polymers1,0032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-12 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.686, 102.808, 101.554
Angle α, β, γ (deg.)90.000, 91.289, 90.000
Int Tables number4
Space group name H-MP1211

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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: 33855.574 Da / Num. of mol.: 4 / Mutation: G143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical
ChemComp-4WI / (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide / PF-07321332, bound form / nirmatrelvir, bound form / Paxlovid, bound form


Mass: 501.542 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H34F3N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M MES, pH 6.7, 5% v/v DMSO, 8% w/v PEG4000, 30% w/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7566
pseudo-merohedral22-h,-k,l20.2434
ReflectionResolution: 1.66→101.53 Å / Num. obs: 74929 / % possible obs: 46.1 % / Redundancy: 3.2 % / CC1/2: 0.968 / Net I/σ(I): 3.7
Reflection shellResolution: 1.66→1.72 Å / Num. unique obs: 112 / CC1/2: 0.463

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7mbg

7mbg


Resolution: 1.664→101.528 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.865 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.216 / SU B: 2.058 / SU ML: 0.069 / Average fsc free: 0.9659 / Average fsc work: 0.9769 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.044
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2506 3690 4.925 %
Rwork0.2077 71238 -
all0.21 --
obs-74928 46.108 %
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: 19.413 Å2
Baniso -1Baniso -2Baniso -3
1--1.973 Å2-0 Å2-0.318 Å2
2---3.408 Å2-0 Å2
3---5.381 Å2
Refinement stepCycle: LAST / Resolution: 1.664→101.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9356 0 144 639 10139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0139731
X-RAY DIFFRACTIONr_bond_other_d0.0030.0159018
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.64413265
X-RAY DIFFRACTIONr_angle_other_deg1.2541.57620723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.79251209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3622.759493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.949151543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3831544
X-RAY DIFFRACTIONr_chiral_restr0.0910.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211180
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022288
X-RAY DIFFRACTIONr_nbd_refined0.2180.22047
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.29339
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24453
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4150.2653
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1910.226
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.241
X-RAY DIFFRACTIONr_nbd_other0.2350.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3950.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1490.22
X-RAY DIFFRACTIONr_mcbond_it1.4842.0324839
X-RAY DIFFRACTIONr_mcbond_other1.4842.0324838
X-RAY DIFFRACTIONr_mcangle_it2.2643.0526041
X-RAY DIFFRACTIONr_mcangle_other2.2643.0526042
X-RAY DIFFRACTIONr_scbond_it1.4752.0854892
X-RAY DIFFRACTIONr_scbond_other1.4752.0854893
X-RAY DIFFRACTIONr_scangle_it2.2253.1037210
X-RAY DIFFRACTIONr_scangle_other2.2253.1037211
X-RAY DIFFRACTIONr_lrange_it6.28524.410685
X-RAY DIFFRACTIONr_lrange_other6.06124.27910560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.664-1.7070.45520.25349X-RAY DIFFRACTION0.4267
1.707-1.7540.274110.243216X-RAY DIFFRACTION1.9435
1.754-1.8050.293180.273552X-RAY DIFFRACTION5.0026
1.805-1.860.254530.2591308X-RAY DIFFRACTION12.3862
1.86-1.9210.297980.2422068X-RAY DIFFRACTION20.1977
1.921-1.9890.2741440.2473163X-RAY DIFFRACTION31.9363
1.989-2.0640.2541930.253985X-RAY DIFFRACTION41.7842
2.064-2.1480.2492130.2384377X-RAY DIFFRACTION47.8823
2.148-2.2440.2612310.224564X-RAY DIFFRACTION51.8996
2.244-2.3530.282760.2324611X-RAY DIFFRACTION55.6163
2.353-2.480.2852230.234904X-RAY DIFFRACTION60.8113
2.48-2.6310.2732580.2255341X-RAY DIFFRACTION70.3569
2.631-2.8120.2383020.225515X-RAY DIFFRACTION77.8715
2.812-3.0370.2352930.2095686X-RAY DIFFRACTION86.1776
3.037-3.3270.2782890.2035778X-RAY DIFFRACTION94.4868
3.327-3.7190.262990.1995337X-RAY DIFFRACTION97.1222
3.719-4.2930.2282790.1784777X-RAY DIFFRACTION98.4041
4.293-5.2560.2412570.1784021X-RAY DIFFRACTION98.3222
5.256-7.4230.2861460.2223206X-RAY DIFFRACTION99.3185

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