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- PDB-7ntt: Crystal structure of the SARS-CoV-2 Main Protease -

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Basic information

Entry
Database: PDB / ID: 7ntt
TitleCrystal structure of the SARS-CoV-2 Main Protease
Components3C-like proteinase
KeywordsVIRAL PROTEIN / 3CLpro / main protease / SARS-CoV-2 / 2019-nCov
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 / 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 / SARS-CoV-2 modulates host translation machinery / 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 / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
Similarity search - Function
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 / Carbamoyl-phosphate synthase subdomain signature 2. ...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 / 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 / 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
FORMIC ACID / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.743 Å
AuthorsDupre, E. / Villeret, V. / Hanoulle, X.
CitationJournal: To Be Published
Title: Crystal structure of the SARS-CoV-2 Main Protease
Authors: Dupre, E. / Villeret, V. / Hanoulle, X.
History
DepositionMar 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)67,7665
Polymers67,6512
Non-polymers1153
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-30 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.760, 53.980, 114.350
Angle α, β, γ (deg.)90.000, 101.180, 90.000
Int Tables number4
Space group name H-MP1211

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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: 33825.547 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M NaFormate, 20% PEG 3350, 10% DMSO, 10% Glycerol

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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: 1.743→48.64 Å / Num. obs: 52176 / % possible obs: 95 % / Redundancy: 6.2 % / CC1/2: 0.993 / Net I/σ(I): 7.72
Reflection shellResolution: 1.743→1.85 Å / Num. unique obs: 6084 / CC1/2: 0.509 / % possible all: 69.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data reduction
Aimless0.7.4data scaling
MOLREP11.7.03phasing
XDSBUILT=20200417data processing
Cootv0.9.4model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K3T

7k3t


Resolution: 1.743→43.949 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.195 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.147
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2547 2609 5.001 %
Rwork0.2073 49563 -
all0.21 --
obs-52172 95.01 %
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: 29.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.126 Å20 Å2-1.221 Å2
2--0.311 Å20 Å2
3---0.042 Å2
Refinement stepCycle: LAST / Resolution: 1.743→43.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 7 277 5011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134891
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174530
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.6396652
X-RAY DIFFRACTIONr_angle_other_deg1.3531.57610410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8345622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56523.184245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52815786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.421523
X-RAY DIFFRACTIONr_chiral_restr0.0720.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021171
X-RAY DIFFRACTIONr_nbd_refined0.1950.2954
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.24342
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22402
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2251
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.29
X-RAY DIFFRACTIONr_nbd_other0.1720.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1790.21
X-RAY DIFFRACTIONr_mcbond_it2.2772.9072476
X-RAY DIFFRACTIONr_mcbond_other2.2772.9082477
X-RAY DIFFRACTIONr_mcangle_it3.4064.3463102
X-RAY DIFFRACTIONr_mcangle_other3.4064.353103
X-RAY DIFFRACTIONr_scbond_it2.7823.2182415
X-RAY DIFFRACTIONr_scbond_other2.7813.2182412
X-RAY DIFFRACTIONr_scangle_it4.3624.6953550
X-RAY DIFFRACTIONr_scangle_other4.3624.6963551
X-RAY DIFFRACTIONr_lrange_it6.35434.8685382
X-RAY DIFFRACTIONr_lrange_other6.35634.8755383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.743-1.7880.397680.4071293X-RAY DIFFRACTION33.6548
1.788-1.8370.3371940.3253680X-RAY DIFFRACTION99.5887
1.837-1.890.3151910.2953641X-RAY DIFFRACTION99.8177
1.89-1.9480.3021880.2643561X-RAY DIFFRACTION99.8136
1.948-2.0120.261790.243399X-RAY DIFFRACTION99.8605
2.012-2.0830.2551730.2293303X-RAY DIFFRACTION99.8277
2.083-2.1610.2971680.2253180X-RAY DIFFRACTION99.9105
2.161-2.250.2921640.2183110X-RAY DIFFRACTION99.9389
2.25-2.350.2631550.1992947X-RAY DIFFRACTION100
2.35-2.4640.2941480.2062824X-RAY DIFFRACTION100
2.464-2.5970.2611430.2132707X-RAY DIFFRACTION99.9649
2.597-2.7550.2921330.2232522X-RAY DIFFRACTION100
2.755-2.9450.2381270.2072430X-RAY DIFFRACTION100
2.945-3.1810.271190.2022250X-RAY DIFFRACTION99.8735
3.181-3.4840.2371080.2022046X-RAY DIFFRACTION100
3.484-3.8950.207980.1891875X-RAY DIFFRACTION99.9493
3.895-4.4960.213880.1621660X-RAY DIFFRACTION99.9428
4.496-5.5050.197740.1551406X-RAY DIFFRACTION99.8651
5.505-7.7750.264570.1771097X-RAY DIFFRACTION100
7.775-43.9490.238340.19632X-RAY DIFFRACTION99.5516

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