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- PDB-7dpu: SARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-myricetin -

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Basic information

Entry
Database: PDB / ID: 7dpu
TitleSARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-myricetin
Components3C-like proteinase
KeywordsVIRAL PROTEIN / SARS-CoV-2 / 3CLpro / inhibitor / complex / myricetin
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 / 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 / methylation / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / 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 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. / 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
Chem-HER / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSu, H.X. / Zhao, W.F. / Xie, H. / Li, M.J. / Xu, Y.C.
CitationJournal: Nat Commun / Year: 2021
Title: Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease.
Authors: Su, H. / Yao, S. / Zhao, W. / Zhang, Y. / Liu, J. / Shao, Q. / Wang, Q. / Li, M. / Xie, H. / Shang, W. / Ke, C. / Feng, L. / Jiang, X. / Shen, J. / Xiao, G. / Jiang, H. / Zhang, L. / Ye, Y. / Xu, Y.
History
DepositionDec 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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)68,4085
Polymers67,6512
Non-polymers7573
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-17 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.258, 53.798, 115.062
Angle α, β, γ (deg.)90.000, 100.960, 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
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical ChemComp-HER / 7-methoxy-3,5-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one


Mass: 332.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH6, 20% PEG6000, 3% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 52638 / % possible obs: 97.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.046 / Rrim(I) all: 0.122 / Χ2: 0.765 / Net I/av σ(I): 20.182 / Net I/σ(I): 4.9 / Num. measured all: 358834
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.816.71.07150710.760.4431.1610.43795.3
1.81-1.897.10.75351800.8750.3020.8120.45696.8
1.89-1.976.90.47652020.9390.1940.5150.48897.2
1.97-2.076.50.33252370.9630.1390.3610.50697.3
2.07-2.27.10.23352160.9830.0930.2510.55897.6
2.2-2.386.90.1752380.9890.0690.1840.62698
2.38-2.616.70.12553110.9920.0520.1360.71398.2
2.61-2.9970.09553210.9950.0380.1020.92898.6
2.99-3.776.80.0753660.9970.0290.0761.39499
3.77-506.60.05854960.9970.0240.0631.51399.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.68 Å48.57 Å
Translation4.68 Å48.57 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M2N

6m2n


Resolution: 1.75→48.57 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 2586 4.92 %
Rwork0.1647 50017 -
obs0.1664 52603 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.12 Å2 / Biso mean: 23.8307 Å2 / Biso min: 8.77 Å2
Refinement stepCycle: final / Resolution: 1.75→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 0 54 410 5119
Biso mean--23.68 32.11 -
Num. residues----610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.780.27021350.23022473260888
1.78-1.820.24241320.20572742287496
1.82-1.860.22631470.1892746289397
1.86-1.90.23711400.18252731287197
1.9-1.950.22741590.17152748290797
1.95-20.20221570.16762764292197
2-2.060.20781270.16462749287697
2.06-2.130.21651530.16472761291498
2.13-2.20.20651540.16272781293598
2.2-2.290.20651560.16142757291398
2.29-2.390.23971370.16692828296598
2.39-2.520.22341410.17072777291898
2.52-2.680.22191420.17112854299699
2.68-2.880.18241250.16972833295899
2.88-3.180.18381460.16552838298499
3.18-3.630.17961590.152829298899
3.64-4.580.16291380.1412863300199
4.58-48.570.18131380.17082943308199
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)
11.0912-0.1040.97191.6642-0.01842.3009-0.12020.11830.1314-0.03850.0319-0.1335-0.20460.1750.08090.1165-0.00370.01690.13760.00520.12232.810220.477837.7158
21.4753-0.48591.05783.852-1.34523.7906-0.23590.14940.3730.18470.0447-0.7678-0.28340.54520.2020.1778-0.0372-0.03410.2637-0.02260.329118.523622.187249.6299
30.97120.14490.86163.2020.38321.9828-0.07220.08030.1128-0.02220.0843-0.093-0.18920.1316-0.02060.0838-0.00350.01370.1189-0.00060.11221.070218.564640.6963
41.47781.1150.84671.30260.40980.89910.08540.0377-0.15570.1046-0.0184-0.16210.02580.0965-0.06940.09590.01460.02010.1126-0.0050.1053-0.68456.120944.3039
52.4062-0.44160.09192.43020.42452.51650.0485-0.1209-0.33390.09830.03690.19730.3394-0.3002-0.08890.1788-0.0254-0.00520.18450.02420.2084-20.439-7.195142.5194
63.99390.22820.27913.21090.21683.73270.1060.2668-0.1636-0.2439-0.05770.0420.2999-0.0174-0.02730.14860.0051-0.0070.1571-0.01210.1139-15.9414-5.030935.254
70.18370.3966-0.04640.8564-0.10010.0117-0.0788-0.1244-0.0410.0982-0.03980.04590.0216-0.08560.11671.05940.37120.43080.66540.17091.0941-19.204616.596431.3212
81.1651-0.6020.52712.1509-0.52961.4734-0.0373-0.04780.08550.01270.03050.1909-0.127-0.15790.01270.12430.01990.02360.1096-0.00890.0996-18.690223.31513.2007
90.3903-0.48580.8843.8774-0.14562.2951-0.0124-0.0085-0.07710.02490.0156-0.05560.0770.04330.00290.0950.0188-0.00250.126-0.01780.1189-8.785812.280717.0556
102.1057-1.17540.79471.4189-0.49120.80180.1005-0.0021-0.1967-0.1626-0.01490.17470.0759-0.0046-0.0980.14820.01170.01340.1494-0.00560.1238-9.91625.119512.3785
112.52550.62910.17181.9756-0.48512.03190.02420.0002-0.1761-0.0303-0.0319-0.01460.23430.21090.00150.14320.05320.02140.1578-0.00340.12566.8906-7.53617.9467
122.00094.11822.55565.158-4.80929.531-0.52040.11060.1888-0.1322-0.2637-0.0874-0.6669-0.25430.77340.3901-0.06560.01090.3415-0.00670.32556.450919.311524.2516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )A1 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 70 )A44 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 155 )A71 - 155
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 213 )A156 - 213
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 260 )A214 - 260
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 302 )A261 - 302
7X-RAY DIFFRACTION7chain 'A' and (resid 303 through 304 )A303 - 304
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 99 )B1 - 99
9X-RAY DIFFRACTION9chain 'B' and (resid 100 through 155 )B100 - 155
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 213 )B156 - 213
11X-RAY DIFFRACTION11chain 'B' and (resid 214 through 302 )B214 - 302
12X-RAY DIFFRACTION12chain 'B' and (resid 303 through 306 )B303 - 306

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