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- PDB-7e18: Crystal structure of SAR-CoV-2 3CL protease complex with inhibito... -

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Basic information

Entry
Database: PDB / ID: 7.0E+18
TitleCrystal structure of SAR-CoV-2 3CL protease complex with inhibitor YH-53
ComponentsReplicase polyprotein 1ab
KeywordsHYDROLASE / SARS-CoV-2 3CL protease
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 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 ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 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 / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / : / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Lipocalin signature. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 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 3Ecto domain profile. / : / 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.
Similarity search - Domain/homology
Chem-HUR / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSenda, M. / Konno, S. / Hayashi, Y. / Senda, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20am0101001 Japan
CitationJournal: J.Med.Chem. / Year: 2022
Title: 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
Authors: Konno, S. / Kobayashi, K. / Senda, M. / Funai, Y. / Seki, Y. / Tamai, I. / Schakel, L. / Sakata, K. / Pillaiyar, T. / Taguchi, A. / Taniguchi, A. / Gutschow, M. / Muller, C.E. / Takeuchi, K. ...Authors: Konno, S. / Kobayashi, K. / Senda, M. / Funai, Y. / Seki, Y. / Tamai, I. / Schakel, L. / Sakata, K. / Pillaiyar, T. / Taguchi, A. / Taniguchi, A. / Gutschow, M. / Muller, C.E. / Takeuchi, K. / Hirohama, M. / Kawaguchi, A. / Kojima, M. / Senda, T. / Shirasaka, Y. / Kamitani, W. / Hayashi, Y.
History
DepositionFeb 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 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: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8369
Polymers33,8261
Non-polymers1,0108
Water2,936163
1
A: Replicase polyprotein 1ab
hetero molecules

A: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,67118
Polymers67,6512
Non-polymers2,02016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5060 Å2
ΔGint20 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.154, 82.673, 51.599
Angle α, β, γ (deg.)90.000, 114.045, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Replicase polyprotein 1ab / pp1ab / ORF1ab polyprotein


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
Gene: rep, 1a-1b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-HUR / N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide


Mass: 575.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H33N5O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 30%(w/v) PEG4000, 0.1 M sodium acetate pH 4.6, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→47.12 Å / Num. obs: 43677 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.8
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.829 / Num. unique obs: 6390

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y2F

6y2f


Resolution: 1.65→29.95 Å / SU ML: 0.1956 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.954
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 2184 5 %
Rwork0.184 41486 -
obs0.1848 43670 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.1 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 69 163 2502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742410
X-RAY DIFFRACTIONf_angle_d1.05033276
X-RAY DIFFRACTIONf_chiral_restr0.0606370
X-RAY DIFFRACTIONf_plane_restr0.0089425
X-RAY DIFFRACTIONf_dihedral_angle_d10.8621380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.2941360.25652584X-RAY DIFFRACTION99.38
1.69-1.730.29241350.25752577X-RAY DIFFRACTION99.52
1.73-1.770.31841360.25972576X-RAY DIFFRACTION99.78
1.77-1.820.32371350.24772566X-RAY DIFFRACTION99.41
1.82-1.870.24571370.20512604X-RAY DIFFRACTION99.6
1.87-1.930.21951350.20232568X-RAY DIFFRACTION99.12
1.93-20.20391370.18872590X-RAY DIFFRACTION99.6
2-2.080.24871350.19382578X-RAY DIFFRACTION99.63
2.08-2.170.1941370.1832604X-RAY DIFFRACTION99.64
2.17-2.290.22691360.18522570X-RAY DIFFRACTION99.52
2.29-2.430.2181380.18952622X-RAY DIFFRACTION99.89
2.43-2.620.20441360.19412591X-RAY DIFFRACTION99.71
2.62-2.880.20711370.1982599X-RAY DIFFRACTION99.49
2.88-3.30.22021360.19232590X-RAY DIFFRACTION99.71
3.3-4.150.15141380.16762615X-RAY DIFFRACTION99.49
4.16-29.950.15991400.15082652X-RAY DIFFRACTION99.5
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9297175023260.5388244487320.1607425178231.675033184850.9406525324023.327047468870.128554829047-0.104761884460.0926302444161-0.1453693168690.000314193469544-0.18670424367-0.4281499220660.22095038852-0.1155656796610.244517224836-0.05960274218940.03287808977860.162490273264-0.01037760258460.2302666815882.090417263759.5914032762612.3452717488
20.9149614787330.1927526243460.4110069041632.83634078491-0.2709035465842.696049507350.0511177570831-0.08517176012990.1730460344560.164800913691-0.103961260011-0.45634765891-0.5339941555590.5454359581720.1068204369670.368918887668-0.1313914001280.01672189294150.286123260288-0.06697910895460.3274084477085.3724574161515.695687352424.498664376
32.25175648485-0.327347681051-0.6390063948533.043108480540.4296503483973.192718243060.006672435619150.04321757562880.0521855498277-0.1548618687430.0121403512203-0.0150727314684-0.2056465916230.08269342273870.006711909876430.150897190657-0.0293147134109-0.00881292398120.123926577801-0.01591717037550.140050183187-1.946856030980.76787904702411.3333370296
40.9321266410950.4407796954020.008927527819341.230208101240.8842309535253.203660634680.032866155827-0.0496612285051-0.1364268191950.1200225144690.00165804895191-0.07062373230080.1923640482670.0911206078353-0.04548547305870.11362083176-0.0188923053731-1.73076774527E-50.113265490204-0.004123950014370.170367124997-3.6842986915-5.6361191012615.8516813533
52.499715460221.187051798361.654542977682.696016850750.8753124125032.517689396640.122937236304-0.440699938621-0.1140080091410.404580117315-0.2525564777570.375043924850.80317585234-1.263251070290.1320172729150.419580728352-0.2182997779170.05968890316590.467879396599-0.07380452845850.330651460078-18.7979982-20.49611936953.67775353509
65.19857137101-0.01392404407291.652435275614.00316744574-0.4493473333965.37212445416-0.034352682510.2968144846310.0490625678485-0.280738175708-0.0398307633074-0.197250362807-0.05766593185410.08056721902140.08115908333340.168849879909-0.05530052060090.024652711670.221720055177-0.05578890043510.203167424768-9.48096427208-13.3391858052-1.14153400381
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )1 - 431 - 43
22chain 'A' and (resid 44 through 100 )44 - 10044 - 100
33chain 'A' and (resid 101 through 155 )101 - 155101 - 155
44chain 'A' and (resid 156 through 213 )156 - 213156 - 213
55chain 'A' and (resid 214 through 274 )214 - 274214 - 274
66chain 'A' and (resid 275 through 303 )275 - 303275 - 303

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