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Entry
Database: PDB / ID: 6y7m
TitleCrystal structure of the complex resulting from the reaction between the SARS-CoV main protease and tert-butyl (1-((S)-3-cyclohexyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Coronavirus / alpha-ketoamide / antiviral / drug design / viral protease
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 / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / 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 / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / 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 / 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 / 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 / viral protein processing / host cell perinuclear region of cytoplasm / lyase activity / 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 / RNA-directed RNA polymerase activity / 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 / 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 / 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
Similarity search - Domain/homology
Chem-OEW / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, L. / Lin, D. / Hilgenfeld, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchDZIF-TTU01 grant 8011801806 Germany
CitationJournal: Science / Year: 2020
Title: Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.
Authors: Zhang, L. / Lin, D. / Sun, X. / Curth, U. / Drosten, C. / Sauerhering, L. / Becker, S. / Rox, K. / Hilgenfeld, R.
History
DepositionMar 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: 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 1.2Apr 28, 2021Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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
AAA: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5403
Polymers33,8771
Non-polymers6642
Water3,549197
1
AAA: 3C-like proteinase
hetero molecules

AAA: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0816
Polymers67,7532
Non-polymers1,3284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3100 Å2
ΔGint-2 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.905, 82.247, 53.131
Angle α, β, γ (deg.)90.000, 104.465, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-646-

HOH

21AAA-688-

HOH

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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: 33876.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: 1a / Production host: Escherichia coli (E. coli)
References: UniProt: P0C6U8, SARS coronavirus main proteinase
#2: Chemical ChemComp-OEW / ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclohexyl-1-[[(2~{S},3~{R})-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate / Tert-butyl (1-((S)-3-cyclohexyl-1-(((S)-4-(cyclopropylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate


Mass: 585.692 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H43N5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 MES, 6% PEG 6,000, pH 6.0 / PH range: 5.5-6.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.67 Å / Num. obs: 35225 / % possible obs: 99.4 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.028 / Rrim(I) all: 0.056 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5113 / CC1/2: 0.88 / Rpim(I) all: 0.372 / Rrim(I) all: 0.742 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BX4

2bx4


Resolution: 1.9→42.356 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.406 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2576 1700 4.842 %
Rwork0.2062 --
all0.209 --
obs-35112 98.993 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.235 Å2
Baniso -1Baniso -2Baniso -3
1--2.775 Å20 Å21.733 Å2
2--1.732 Å20 Å2
3---0.132 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 46 197 2614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132482
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172238
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.6673375
X-RAY DIFFRACTIONr_angle_other_deg1.451.5985198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8775307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94122.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72115393
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.321151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1351512
X-RAY DIFFRACTIONr_chiral_restr0.1790.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022797
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02524
X-RAY DIFFRACTIONr_nbd_refined0.2140.2515
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22237
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21206
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21203
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2143
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.212
X-RAY DIFFRACTIONr_nbd_other0.1970.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.216
X-RAY DIFFRACTIONr_mcbond_it4.3334.8851228
X-RAY DIFFRACTIONr_mcbond_other4.334.8831227
X-RAY DIFFRACTIONr_mcangle_it5.8657.3111535
X-RAY DIFFRACTIONr_mcangle_other5.8657.3151536
X-RAY DIFFRACTIONr_scbond_it4.8575.4041254
X-RAY DIFFRACTIONr_scbond_other4.8575.4081255
X-RAY DIFFRACTIONr_scangle_it6.97.9151837
X-RAY DIFFRACTIONr_scangle_other6.8987.9191838
X-RAY DIFFRACTIONr_lrange_it9.06159.6282776
X-RAY DIFFRACTIONr_lrange_other9.02759.462754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.5151220.4682371X-RAY DIFFRACTION95.8477
2.003-2.0610.3481240.322336X-RAY DIFFRACTION99.6355
2.061-2.1240.3321130.3372272X-RAY DIFFRACTION99.0037
2.124-2.1940.2851100.252207X-RAY DIFFRACTION99.7847
2.194-2.2710.4151130.3272071X-RAY DIFFRACTION97.2395
2.271-2.3560.3131180.2582056X-RAY DIFFRACTION99.5877
2.356-2.4520.344840.2331998X-RAY DIFFRACTION99.2847
2.452-2.5610.301920.2341910X-RAY DIFFRACTION99.8006
2.561-2.6860.2991000.2251822X-RAY DIFFRACTION99.5339
2.686-2.8310.258800.2161744X-RAY DIFFRACTION99.9452
2.831-3.0020.253830.1991646X-RAY DIFFRACTION99.8268
3.002-3.2090.273770.2131544X-RAY DIFFRACTION99.4479
3.209-3.4650.243640.2021432X-RAY DIFFRACTION98.4211
3.465-3.7950.312640.1961320X-RAY DIFFRACTION98.156
3.795-4.2410.196610.1591195X-RAY DIFFRACTION99.1318
4.241-4.8940.161630.1321063X-RAY DIFFRACTION99.5579
4.894-5.9850.229500.154900X-RAY DIFFRACTION99.2685
5.985-8.4280.224360.176699X-RAY DIFFRACTION98.7903

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