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- PDB-7dpv: SARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-dihyd... -

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Basic information

Entry
Database: PDB / ID: 7dpv
TitleSARS-CoV-2 3CL protease (3CLpro) in complex with 7-O-methyl-dihydromyricetin
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / methylation / 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 / 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 / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 / 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 / Trypsin-like serine proteases / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Thrombin, subunit H / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-HF0 / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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
A: 3C-like proteinase
B: 3C-like proteinase
C: 3C-like proteinase
D: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6398
Polymers135,3024
Non-polymers1,3374
Water5,332296
1
A: 3C-like proteinase
C: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3204
Polymers67,6512
Non-polymers6692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-12 kcal/mol
Surface area24650 Å2
MethodPISA
2
B: 3C-like proteinase
hetero molecules

D: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3204
Polymers67,6512
Non-polymers6692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area2320 Å2
ΔGint-11 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.647, 68.050, 102.394
Angle α, β, γ (deg.)90.000, 90.010, 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.: 4
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-HF0 / (2S,3S)-3,5-dihydroxy-7-methoxy-2-(3,4,5-trihydroxyphenyl)chroman-4-one


Mass: 334.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM 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: May 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 50801 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.144 / Rrim(I) all: 0.319 / Χ2: 0.521 / Net I/σ(I): 3.5 / Num. measured all: 208908
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.433.10.80849120.6810.490.9490.43397.1
2.43-2.533.30.80550290.710.4730.9380.43399
2.53-2.653.50.85250020.7040.4780.9820.43699.5
2.65-2.793.70.8451040.7270.4580.9610.4499.8
2.79-2.964.10.72850810.7710.3770.8230.44399.9
2.96-3.194.50.60250630.9160.2960.6730.46299.9
3.19-3.514.60.38451230.9540.1880.4290.498100
3.51-4.024.60.22851070.980.1110.2550.575100
4.02-5.064.90.12751230.9920.060.140.637100
5.06-504.70.08952570.9930.0430.0990.70499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.96 Å44.34 Å
Translation3.96 Å44.34 Å

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Processing

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

6m2n


Resolution: 2.35→44.34 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2457 4.84 %
Rwork0.2021 48289 -
obs0.2037 50746 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.91 Å2 / Biso mean: 41.1005 Å2 / Biso min: 13.84 Å2
Refinement stepCycle: final / Resolution: 2.35→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8605 0 96 296 8997
Biso mean--65 34.22 -
Num. residues----1163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.390.27441070.25642464257192
2.39-2.440.32071560.24362605276197
2.44-2.50.29581170.25262701281899
2.5-2.550.30281660.23272617278399
2.55-2.620.25661250.23172699282499
2.62-2.690.29641080.221526892797100
2.69-2.770.2441490.232126742823100
2.77-2.860.25581250.22827212846100
2.86-2.960.24261330.21927052838100
2.96-3.080.24221380.210226872825100
3.08-3.220.2741450.214226822827100
3.22-3.390.20321350.203527142849100
3.39-3.60.26421020.196727112813100
3.6-3.880.2181460.183527072853100
3.88-4.270.21831660.169227032869100
4.27-4.880.16451740.162626912865100
4.88-6.150.2021360.19527362872100
6.15-44.340.25491290.19482783291299
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)
18.60940.21860.6041.81872.19155.7329-0.3645-0.2719-0.7198-0.43690.4048-0.9517-0.82051.7398-0.23550.5549-0.24870.11970.9840.04010.8888-0.2582-33.9719-53.1709
29.20890.0656-1.87525.08760.18064.5496-0.26110.9136-0.3069-0.8830.70850.42990.0625-0.2747-0.54610.4186-0.1449-0.09040.5022-0.02140.3484-11.61-37.61-55.91
31.30720.660.06244.1029-0.2893.28450.0241-0.07340.0164-0.0757-0.01270.1325-0.0329-0.2007-0.00770.21590.0026-0.00420.1639-0.01160.1444-14.841115.9362-9.1494
40.1484-0.03220.01314.18111.36440.7738-0.0406-0.0222-0.04730.1280.06150.02710.01160.0460.00380.4373-0.0587-0.02520.2148-0.00310.2543-15.3774-12.3066-20.5177
50.98960.3153-0.1915.3346-1.22663.8612-0.03080.0699-0.0824-0.03630.08780.22370.2374-0.1295-0.05750.18650.01660.01950.1707-0.01230.1585-58.5896-26.9216-43.5257
60.66150.77530.28516.33090.41351.59230.04-0.040.09150.30230.01240.2074-0.0923-0.2748-0.02820.3650.03810.06150.2092-0.02070.1737-61.5092-13.4726-35.035
75.1367-1.2571-0.34143.3511.99155.09920.03990.1741-0.1081-0.16920.0909-0.07830.17990.2508-0.13310.42080.02770.04190.1329-0.01150.2666-58.67018.7845-30.8317
82.7821-1.56481.07873.2595-1.02942.5745-0.0835-0.0475-0.12280.04170.04990.01570.03240.0590.05620.183-0.04020.06260.17950.02450.1375-11.6069-4.28712.2079
93.55031.27490.50172.4677-0.11493.2873-0.0049-0.1766-0.4925-0.01910.0548-0.2880.53770.3093-0.04190.3950.06170.04170.1839-0.00280.207-10.3654-7.869518.128
108.39910.39332.28762.01780.38232.53270.16220.7392-0.0294-0.6744-0.046-0.33020.24450.1414-0.05490.7237-0.03540.04650.30930.00620.3392-20.8644-14.28285.7196
115.3206-0.08782.13323.1414-1.33434.8681-0.11720.4496-0.2952-0.15140.21620.34450.4958-0.293-0.13730.3459-0.07620.03860.2623-0.0040.1959-24.2661-11.24368.2843
125.52670.0515-0.06443.18530.36764.2789-0.4660.26270.3256-0.410.29741.42490.8754-2.07910.04990.6478-0.3449-0.07211.19830.08640.829-44.9796-9.5666-3.1602
136.45-1.79811.78523.4145-2.35843.5142-0.54390.81050.7513-1.11080.8642-0.91890.3212-0.3845-0.19720.4939-0.20960.12440.60560.10310.4316-32.7413-3.3738-4.578
142.9689-1.7688-1.13363.56531.98732.9369-0.00750.0427-0.02660.1324-0.05270.0012-0.0259-0.1272-0.00620.2706-0.0256-0.04470.1885-0.02410.1267-32.7112-37.8135-39.0022
153.87041.0598-0.47883.1240.89093.68920.0547-0.22730.46930.1305-0.02140.2035-0.5731-0.4242-0.02930.39010.0715-0.01270.18940.01270.2023-34.0064-34.0868-33.0445
169.18826.3048-4.25575.1681-1.00055.8966-0.16960.95091.1616-0.5719-0.01390.7068-0.491-0.21640.20780.5887-0.0164-0.05830.24420.00270.3512-23.4438-27.7561-45.453
175.63370.03-2.23763.11051.30955.1277-0.11410.51260.2193-0.15180.2466-0.437-0.47190.2825-0.14620.3311-0.061-0.01970.2695-0.02230.2228-19.9351-31.046-42.8358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 214 through 273 )D214 - 273
2X-RAY DIFFRACTION2chain 'D' and (resid 274 through 299 )D274 - 301
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 180 )A2 - 180
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 300 )A181 - 300
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 129 )B2 - 129
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 213 )B130 - 213
7X-RAY DIFFRACTION7chain 'B' and (resid 214 through 300 )B214 - 300
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 43 )C1 - 43
9X-RAY DIFFRACTION9chain 'C' and (resid 44 through 129 )C44 - 129
10X-RAY DIFFRACTION10chain 'C' and (resid 130 through 144 )C130 - 144
11X-RAY DIFFRACTION11chain 'C' and (resid 145 through 214 )C145 - 214
12X-RAY DIFFRACTION12chain 'C' and (resid 215 through 273 )C215 - 273
13X-RAY DIFFRACTION13chain 'C' and (resid 274 through 301 )C274 - 301
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 43 )D1 - 43
15X-RAY DIFFRACTION15chain 'D' and (resid 44 through 129 )D44 - 129
16X-RAY DIFFRACTION16chain 'D' and (resid 130 through 144 )D130 - 144
17X-RAY DIFFRACTION17chain 'D' and (resid 145 through 213 )D145 - 213

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