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- PDB-7vtc: Crystal structure of MERS main protease in complex with PF07321332 -

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Basic information

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


host cell membrane / viral genome replication / transferase activity / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / membrane => GO:0016020 / single-stranded RNA binding / host cell perinuclear region of cytoplasm ...host cell membrane / viral genome replication / transferase activity / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / membrane => GO:0016020 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / zinc ion binding / identical protein binding
Similarity search - Function
Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-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 / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. ...Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-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 / 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53865625155 Å
AuthorsLin, C. / Zhong, F.L. / Zhou, X.L. / Zhang, J. / Li, 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 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,9723
Polymers70,4702
Non-polymers5021
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-14 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.422, 93.243, 97.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 3C-like proteinase


Mass: 35235.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: T2B9A8, ubiquitinyl hydrolase 1, 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.: 1 / 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.: 48 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium formate, 0.1M BICINE pH8.5 20% PEG5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.53865625155→48.79 Å / Num. obs: 23783 / % possible obs: 92 % / Redundancy: 5.7 % / Biso Wilson estimate: 47.576322279 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.6
Reflection shellResolution: 2.54→2.68 Å / Rmerge(I) obs: 1.228 / Num. unique obs: 2227

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DR8

7dr8


Resolution: 2.53865625155→48.789 Å / SU ML: 0.394013367685 / Cross valid method: NONE / σ(F): 1.33777064197 / Phase error: 26.420780996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241685952321 3755 8.48549218114 %
Rwork0.191838754761 40497 -
obs0.196038292879 23727 91.047877703 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.4234129007 Å2
Refinement stepCycle: LAST / Resolution: 2.53865625155→48.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 35 48 4552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008620418214634615
X-RAY DIFFRACTIONf_angle_d1.017213543766310
X-RAY DIFFRACTIONf_chiral_restr0.0532122988528736
X-RAY DIFFRACTIONf_plane_restr0.00676127423743801
X-RAY DIFFRACTIONf_dihedral_angle_d4.464142428862709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5387-2.57080.3746489778411660.3104484499051629X-RAY DIFFRACTION99.4459833795
2.5708-2.60460.3654392329881390.3263193442591692X-RAY DIFFRACTION99.1337303736
2.6046-2.64030.276495055711440.330052439403510X-RAY DIFFRACTION71.2998712999
2.678-2.7180.408129483833710.365389633325782X-RAY DIFFRACTION80.3958529689
2.718-2.76040.3714526675441590.2988922798311617X-RAY DIFFRACTION99.5515695067
2.7604-2.80570.3149014375821360.2663019386871639X-RAY DIFFRACTION99.2729306488
2.8057-2.85410.3514701341831680.2592439022781638X-RAY DIFFRACTION99.5041322314
2.8541-2.9060.3334032469231510.2600475674081641X-RAY DIFFRACTION99.4450610433
2.906-2.96190.2783577627621580.2635776264831620X-RAY DIFFRACTION99.7755331089
2.9619-3.02230.333267785681510.2585515895111641X-RAY DIFFRACTION99.5555555556
3.0223-3.0880.3278456253911480.2444863171921655X-RAY DIFFRACTION99.6132596685
3.088-3.15980.3143281467841290.2446775316451666X-RAY DIFFRACTION99.8331479422
3.1598-3.23880.288346074651690.2266656306911644X-RAY DIFFRACTION99.779856907
3.2388-3.32640.2699967872621510.2154074954091620X-RAY DIFFRACTION99.7746478873
3.3264-3.42420.2657626866451480.2038794772481629X-RAY DIFFRACTION99.7194163861
3.4242-3.53470.2557585153511430.202429529171668X-RAY DIFFRACTION99.6149614961
3.5347-3.6610.2367578182581640.1940526296431626X-RAY DIFFRACTION99.4997220678
3.661-3.80760.2361643966461580.1878003402331633X-RAY DIFFRACTION99.5
3.8076-3.98080.2323819301381540.173649923411635X-RAY DIFFRACTION98.9491150442
3.9808-4.19050.2159597492311460.1547864453481635X-RAY DIFFRACTION98.7798114254
4.1905-4.45290.1836093769471540.1479880592831630X-RAY DIFFRACTION98.3461962514
4.4529-4.79650.159835693681500.1370756299761607X-RAY DIFFRACTION98.3212087297
4.7965-5.27860.1765055352991540.1426853499651586X-RAY DIFFRACTION97.4789915966
5.2786-6.04130.2166718055121550.1687981435961623X-RAY DIFFRACTION98.5587583149
6.0413-7.60670.2642181662031390.164813913541637X-RAY DIFFRACTION98.6118822876
7.6067-48.7890.16298525781500.1372499710511594X-RAY DIFFRACTION96.94274597

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