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- PDB-7ntq: Crystal structure of the SARS-CoV-2 Main Protease complexed with ... -

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Entry
Database: PDB / ID: 7ntq
TitleCrystal structure of the SARS-CoV-2 Main Protease complexed with N-(pyridin-3-ylmethyl)thioformamide
Components3C-like proteinase
KeywordsVIRAL PROTEIN / 3CLpro / main protease / SARS-CoV-2 / 2019-nCov / inhibitor
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 / endonuclease 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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / 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 / regulation of autophagy / host cell perinuclear region of cytoplasm / 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 / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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. / : / : / 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 / Thrombin, subunit H / 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 / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
N-(pyridin-3-ylmethyl)thioformamide / FORMIC ACID / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.495 Å
AuthorsDupre, E. / Villeret, V. / Hanoulle, X.
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Novel dithiocarbamates selectively inhibit 3CL protease of SARS-CoV-2 and other coronaviruses.
Authors: Brier, L. / Hassan, H. / Hanoulle, X. / Landry, V. / Moschidi, D. / Desmarets, L. / Rouille, Y. / Dumont, J. / Herledan, A. / Warenghem, S. / Piveteau, C. / Carre, P. / Ikherbane, S. / ...Authors: Brier, L. / Hassan, H. / Hanoulle, X. / Landry, V. / Moschidi, D. / Desmarets, L. / Rouille, Y. / Dumont, J. / Herledan, A. / Warenghem, S. / Piveteau, C. / Carre, P. / Ikherbane, S. / Cantrelle, F.X. / Dupre, E. / Dubuisson, J. / Belouzard, S. / Leroux, F. / Deprez, B. / Charton, J.
History
DepositionMar 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,76017
Polymers33,8261
Non-polymers93416
Water3,891216
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,51934
Polymers67,6512
Non-polymers1,86832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7120 Å2
ΔGint-27 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.920, 52.910, 44.900
Angle α, β, γ (deg.)90.000, 102.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-668-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33825.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pHisSUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTC1, SARS coronavirus main proteinase

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Non-polymers , 5 types, 232 molecules

#2: Chemical ChemComp-35J / N-(pyridin-3-ylmethyl)thioformamide


Mass: 152.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.97 Å3/Da / Density % sol: 37.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M NaFormate, 20% PEG 3350, 10% Glycerol, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978564 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564 Å / Relative weight: 1
ReflectionResolution: 1.49→47.84 Å / Num. obs: 42066 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 9.77
Reflection shellResolution: 1.49→1.59 Å / Num. unique obs: 6311 / CC1/2: 0.51 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data reduction
Aimless0.7.4data scaling
MOLREP11.7.03phasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K3T

7k3t


Resolution: 1.495→43.809 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.002 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2132 2104 5.002 %
Rwork0.1706 39961 -
all0.173 --
obs-42065 98.712 %
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: 23.691 Å2
Baniso -1Baniso -2Baniso -3
1-0.473 Å2-0 Å2-0.229 Å2
2--0.034 Å20 Å2
3----0.364 Å2
Refinement stepCycle: LAST / Resolution: 1.495→43.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 44 216 2628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172291
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.6393323
X-RAY DIFFRACTIONr_angle_other_deg1.4581.5775250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0323.058121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3715389
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.764151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9731511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02590
X-RAY DIFFRACTIONr_nbd_refined0.2330.2444
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22106
X-RAY DIFFRACTIONr_nbtor_refined0.170.21200
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21171
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2148
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3020.218
X-RAY DIFFRACTIONr_nbd_other0.1780.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2780.227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.495-1.5340.3431300.3362462X-RAY DIFFRACTION82.6004
1.534-1.5760.3621530.3012902X-RAY DIFFRACTION100
1.576-1.6210.3421490.2812833X-RAY DIFFRACTION100
1.621-1.6710.3021430.2622716X-RAY DIFFRACTION100
1.671-1.7260.2281400.2262660X-RAY DIFFRACTION100
1.726-1.7860.2571350.2082569X-RAY DIFFRACTION100
1.786-1.8540.2411310.1952485X-RAY DIFFRACTION100
1.854-1.9290.191260.1662398X-RAY DIFFRACTION100
1.929-2.0150.2221210.1682291X-RAY DIFFRACTION100
2.015-2.1130.2231160.1722204X-RAY DIFFRACTION100
2.113-2.2270.2311100.1682095X-RAY DIFFRACTION100
2.227-2.3620.2151030.1641958X-RAY DIFFRACTION100
2.362-2.5250.234980.1621865X-RAY DIFFRACTION99.9491
2.525-2.7270.218920.1631741X-RAY DIFFRACTION100
2.727-2.9870.205840.1631603X-RAY DIFFRACTION100
2.987-3.3380.173760.1531447X-RAY DIFFRACTION99.9344
3.338-3.8520.182680.1451285X-RAY DIFFRACTION100
3.852-4.7120.173580.1291102X-RAY DIFFRACTION100
4.712-6.6410.254440.167847X-RAY DIFFRACTION100
6.641-43.8090.136270.174498X-RAY DIFFRACTION99.8099

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