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- PDB-7vlo: Crystal structure of SARS coronavirus main protease in complex wi... -

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Entry
Database: PDB / ID: 7vlo
TitleCrystal structure of SARS coronavirus main protease in complex with PF07321332
Components3C-like proteinase
KeywordsVIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / host cell endoplasmic reticulum / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 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 / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / methylation / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / identical protein binding / membrane
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / 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 ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / 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 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / 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. / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-4WI / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0227 Å
AuthorsLin, C. / Zhong, F.L. / Zhou, X.L. / Li, J. / Zhang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2022
Title: Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate PF-07321332.
Authors: Li, J. / Lin, C. / Zhou, X. / Zhong, F. / Zeng, P. / Yang, Y. / Zhang, Y. / Yu, B. / Fan, X. / McCormick, P.J. / Fu, R. / Fu, Y. / Jiang, H. / Zhang, J.
History
DepositionOct 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,3434
Polymers66,3402
Non-polymers1,0032
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-8 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.464, 60.461, 68.137
Angle α, β, γ (deg.)91.921, 102.421, 108.764
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 33169.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome-related coronavirus
Gene: 1a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0C6U8, 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.: 2 / Source method: obtained synthetically / Formula: C23H34F3N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antivirus, protease inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.17 Å3/Da / Density % sol: 61.2 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M Hepes pH7.5, 10% PEG8000, 8% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.02→30.08 Å / Num. obs: 50908 / % possible obs: 95.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.5881276732 Å2 / Rmerge(I) obs: 0.026 / Net I/σ(I): 9.8
Reflection shellResolution: 2.02→2.13 Å / Rmerge(I) obs: 0.243 / Num. unique obs: 7508

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EO8

7eo8


Resolution: 2.0227→30.0793 Å / SU ML: 0.212936796701 / Cross valid method: NONE / σ(F): 2.01010185232 / Phase error: 28.6103282647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23435923961 3754 3.9077707802 %
Rwork0.203790349039 92311 -
obs0.204956739489 50844 90.3664891916 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.0737829164 Å2
Refinement stepCycle: LAST / Resolution: 2.0227→30.0793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 0 70 67 4562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007368781005564600
X-RAY DIFFRACTIONf_angle_d0.9363752296546294
X-RAY DIFFRACTIONf_chiral_restr0.0515310619926728
X-RAY DIFFRACTIONf_plane_restr0.00613452754317811
X-RAY DIFFRACTIONf_dihedral_angle_d5.112285771062661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0227-2.04830.3510371083891320.2966520804813306X-RAY DIFFRACTION85.9070464768
2.0483-2.07520.3271183832831330.280537751293225X-RAY DIFFRACTION86.1467419189
2.0752-2.10370.2956800553881350.2620325895643317X-RAY DIFFRACTION87.6587100051
2.1037-2.13370.2835329022051390.2528208228783474X-RAY DIFFRACTION90.4154154154
2.1337-2.16560.2557738339961370.237940688673405X-RAY DIFFRACTION91.0071942446
2.1656-2.19940.2989853677981430.2436084063213488X-RAY DIFFRACTION92.2510162602
2.1994-2.23540.2791918002621410.2306665832223533X-RAY DIFFRACTION93.2487309645
2.2354-2.2740.238929672682760.2310116332612009X-RAY DIFFRACTION53.6817713697
2.274-2.31530.3020340785811470.222828156313629X-RAY DIFFRACTION94.4
2.3153-2.35980.2594918398391480.2345845373833556X-RAY DIFFRACTION94.6830265849
2.3598-2.4080.2817799704331480.2303763355653610X-RAY DIFFRACTION94.8032290616
2.408-2.46030.2763525353091430.2319924342233468X-RAY DIFFRACTION93.7922077922
2.4603-2.51750.2840228953731530.2364977554593709X-RAY DIFFRACTION94.1951219512
2.5175-2.58040.324094895491390.2339781777983412X-RAY DIFFRACTION93.6445147679
2.5804-2.65020.2838179349741450.2435268991233540X-RAY DIFFRACTION93.3857070451
2.6502-2.72810.2748553806061450.234312844973545X-RAY DIFFRACTION92.8535480624
2.7281-2.81610.3295288720351430.2423191465833464X-RAY DIFFRACTION92.2506393862
2.8161-2.91660.2533974245761450.2434731177543501X-RAY DIFFRACTION92.6792069141
2.9166-3.03330.2725271934341460.2418730128823476X-RAY DIFFRACTION92.0223577236
3.0333-3.17120.27391837471410.2308442739143481X-RAY DIFFRACTION92.5869120654
3.1712-3.33820.2435266165631420.2347454318623504X-RAY DIFFRACTION92.1172309247
3.3382-3.54710.2864436814071440.2159368873333496X-RAY DIFFRACTION91.641490433
3.5471-3.82040.222358929191360.1908967956723409X-RAY DIFFRACTION91.2249099331
3.8204-4.2040.1628493203581390.1720687664153461X-RAY DIFFRACTION90.9550277918
4.204-4.81020.1737861444461400.1456486948223409X-RAY DIFFRACTION90.4895461499
4.8102-6.05220.1675506412111360.1689598657293424X-RAY DIFFRACTION90.0809716599
6.0522-30.07930.1792066953551380.1526233103933460X-RAY DIFFRACTION91.6921508665

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