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- PDB-7ntw: Crystal structure of the SARS-CoV-2 Main Protease with a Zinc ion... -

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Entry
Database: PDB / ID: 7ntw
TitleCrystal structure of the SARS-CoV-2 Main Protease with a Zinc ion coordinated in the active site
Components3C-like proteinase
KeywordsVIRAL PROTEIN / SARS-CoV-2 / main protease / Zinc / nCoV-2019
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 / methylation / double membrane vesicle viral factory outer membrane ...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 / methylation / 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 / SARS-CoV-2 modulates host translation machinery / 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 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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. / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 (BetaCoV) Nsp1 C-terminal 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 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 (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / 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. / 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. / 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
FORMIC ACID / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.815 Å
AuthorsDupre, E. / Villeret, V. / Hanoulle, X.
CitationJournal: To Be Published
Title: Crystal structure of the SARS-CoV-2 Main Protease with a Zinc ion coordinated in the active site
Authors: Dupre, E. / Villeret, V. / Hanoulle, X.
History
DepositionMar 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,34612
Polymers33,8261
Non-polymers52111
Water1,74797
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,69324
Polymers67,6512
Non-polymers1,04222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6420 Å2
ΔGint-124 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.310, 53.680, 44.720
Angle α, β, γ (deg.)90.000, 101.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-572-

HOH

31A-580-

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, 108 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.97 Å3/Da / Density % sol: 37.62 %
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: 1.815→48.37 Å / Num. obs: 23721 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 12.8
Reflection shellResolution: 1.815→1.85 Å / Num. unique obs: 1352 / CC1/2: 0.423 / % possible all: 94.2

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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: 1.815→48.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.057 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.257 1186 5 %
Rwork0.1966 22535 -
all0.2 --
obs-23721 99.114 %
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: 38.006 Å2
Baniso -1Baniso -2Baniso -3
1-1.697 Å2-0 Å20.097 Å2
2--0.197 Å20 Å2
3----1.782 Å2
Refinement stepCycle: LAST / Resolution: 1.815→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 27 97 2475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172270
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6393307
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5775209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8825308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4722.975121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2115391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8371512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
X-RAY DIFFRACTIONr_nbd_refined0.210.2504
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22169
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21181
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.292
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.227
X-RAY DIFFRACTIONr_nbd_other0.20.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.210
X-RAY DIFFRACTIONr_mcbond_it2.8363.8611229
X-RAY DIFFRACTIONr_mcbond_other2.8353.8631230
X-RAY DIFFRACTIONr_mcangle_it3.8415.781538
X-RAY DIFFRACTIONr_mcangle_other3.845.7851539
X-RAY DIFFRACTIONr_scbond_it3.2744.1871211
X-RAY DIFFRACTIONr_scbond_other3.2684.171202
X-RAY DIFFRACTIONr_scangle_it4.7796.1321769
X-RAY DIFFRACTIONr_scangle_other4.7796.1341770
X-RAY DIFFRACTIONr_lrange_it6.78446.022653
X-RAY DIFFRACTIONr_lrange_other6.72945.9142639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.815-1.8620.397830.3421584X-RAY DIFFRACTION94.9858
1.862-1.9130.335850.3341610X-RAY DIFFRACTION99.007
1.913-1.9690.344820.2841559X-RAY DIFFRACTION98.915
1.969-2.0290.329800.2631531X-RAY DIFFRACTION98.895
2.029-2.0960.243780.2391477X-RAY DIFFRACTION99.2342
2.096-2.1690.283750.2281435X-RAY DIFFRACTION99.2768
2.169-2.2510.317740.2111394X-RAY DIFFRACTION99.3234
2.251-2.3430.257700.2191331X-RAY DIFFRACTION99.4322
2.343-2.4470.316660.2181263X-RAY DIFFRACTION99.6252
2.447-2.5660.251650.1941229X-RAY DIFFRACTION99.7687
2.566-2.7040.344620.2151182X-RAY DIFFRACTION99.5997
2.704-2.8680.239580.2061097X-RAY DIFFRACTION99.8271
2.868-3.0650.222560.2071055X-RAY DIFFRACTION99.7307
3.065-3.310.312510.203975X-RAY DIFFRACTION99.9026
3.31-3.6250.221470.179896X-RAY DIFFRACTION100
3.625-4.050.223430.161817X-RAY DIFFRACTION100
4.05-4.6730.175390.151732X-RAY DIFFRACTION100
4.673-5.7130.256320.182607X-RAY DIFFRACTION99.8438
5.713-8.0360.318250.179484X-RAY DIFFRACTION100
8.036-48.370.211150.15277X-RAY DIFFRACTION96.6887

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