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- PDB-8gtw: SARS-CoV-2 3CL protease (3CLpro) in complex with compound JZD-26 -

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Basic information

Entry
Database: PDB / ID: 8gtw
TitleSARS-CoV-2 3CL protease (3CLpro) in complex with compound JZD-26
Components3C-like proteinase
KeywordsVIRAL PROTEIN/INHIBITOR / Mpro / VIRAL PROTEIN-INHIBITOR COMPLEX
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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / 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-K9U / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSu, H.X. / Nie, T.Q. / Xie, H. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Development of novel inhibitors against SARS-CoV-2 3CLpro
Authors: Xu, Y.C. / Zang, Y. / Zhou, Y.
History
DepositionSep 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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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)68,7344
Polymers67,6512
Non-polymers1,0832
Water3,423190
1
A: 3C-like proteinase
hetero molecules

B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7344
Polymers67,6512
Non-polymers1,0832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2670 Å2
ΔGint-10 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.616, 81.708, 89.079
Angle α, β, γ (deg.)90.000, 97.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3C-like proteinase / main protease


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)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical ChemComp-K9U / (2S)-4-(3,4-dichlorophenyl)-1-[(2-oxidanylidene-1H-quinolin-4-yl)carbonyl]-N-[3,3,3-tris(fluoranyl)propyl]piperazine-2-carboxamide


Mass: 541.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H21Cl2F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 62946 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.071 / Rrim(I) all: 0.182 / Χ2: 0.79 / Net I/σ(I): 4.2 / Num. measured all: 390051
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.925.51.36262660.7240.6371.5070.49799.8
1.92-1.995.71.03562520.8170.471.1390.50799.8
1.99-2.085.80.85462590.7910.3830.9380.56399.9
2.08-2.195.60.59862500.8430.2750.660.63899.8
2.19-2.336.20.50862910.9530.220.5540.71999.9
2.33-2.516.50.41962580.9740.1770.4560.782100
2.51-2.766.50.37863280.9710.1610.4110.974100
2.76-3.166.80.26462850.9890.1090.2860.976100
3.16-3.996.70.14863470.9930.0620.161.024100
3.99-506.70.09664100.9940.040.1041.0399.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.93 Å44.19 Å
Translation4.93 Å44.19 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.8.3phasing
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M2N

6m2n


Resolution: 1.85→31.56 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 3130 4.98 %
Rwork0.1981 59678 -
obs0.1995 62808 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.57 Å2 / Biso mean: 42.5112 Å2 / Biso min: 22.25 Å2
Refinement stepCycle: final / Resolution: 1.85→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4520 0 261 1 4782
Biso mean--44.61 33.52 -
Num. residues----608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.33951390.2822568270796
1.87-1.910.26931390.267627582897100
1.91-1.940.29961440.259826772821100
1.94-1.970.31041500.246827062856100
1.97-2.010.30081280.247527002828100
2.01-2.050.26461390.242827202859100
2.05-2.10.25721400.228326922832100
2.1-2.150.25321500.218227232873100
2.15-2.20.20861450.216127152860100
2.2-2.260.23511390.217727142853100
2.26-2.330.25811250.212727152840100
2.33-2.40.25821530.213127012854100
2.4-2.490.23431460.215227312877100
2.49-2.590.28671560.201427022858100
2.59-2.70.24811650.204727152880100
2.7-2.850.23461220.214227282850100
2.85-3.020.26981570.207527342891100
3.02-3.260.22391460.212527072853100
3.26-3.580.23031380.20427392877100
3.59-4.10.19841510.177827202871100
4.1-5.160.17881330.161627802913100
5.17-31.560.19521250.16872733285897
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)
12.9325-0.4099-0.82091.47640.53881.66410.0676-0.33410.66020.14860.0874-0.2861-0.07630.0934-0.1640.2313-0.0084-0.02210.2209-0.05460.32670.045325.300929.763
25.20350.9018-0.8612.05860.52962.0851-0.0084-0.88510.50460.62010.0493-0.01860.19850.0614-0.03350.38180.04490.02630.4782-0.15830.3805-13.4627.230944.1575
31.30180.4358-1.13811.4867-0.31721.56990.2284-0.18060.80180.3191-0.0254-0.2888-0.28560.0397-0.11120.3695-0.00790.05240.2993-0.13380.6694-6.541334.715431.8577
42.6536-0.2315-0.24881.4358-0.75951.07790.0452-0.03440.1305-0.0775-0.0392-0.11150.03910.0119-0.0260.2486-0.00650.00410.2289-0.03730.2367-2.579417.01426.6037
51.8554-0.1011-0.15031.88111.15050.59-0.07220.1281-0.24720.1902-0.01060.11620.2838-0.05870.09830.25030.0162-0.04150.2099-0.01520.2106-5.435.46622.3199
61.02560.5385-0.48212.3812-0.1212.6546-0.27760.816-0.44270.02570.18440.21010.1439-0.68520.05960.3827-0.0130.04330.6076-0.16170.4941-2.1777-2.79846.227
72.39030.33980.32734.71610.61211.68590.08020.4146-0.42190.0902-0.0798-0.3410.2281-0.00360.01540.2720.0436-0.0260.3721-0.11760.32455.561-0.281510.6594
82.29650.4614-0.64571.312-0.21451.596-0.08250.20370.3871-0.42790.06770.2410.06290.0150.00790.3099-0.0085-0.01420.23430.05540.3192-30.86525.561215.3112
92.5106-0.3966-0.90671.0470.41111.68310.10920.39640.4007-0.6217-0.0266-0.0456-0.28640.0576-0.02060.5612-0.05450.06510.40090.1260.4793-21.246531.74747.3943
102.46740.08110.15252.05480.27910.32180.00060.09030.118-0.0505-0.00690.06220.0174-0.0041-0.01720.2766-0.01190.00210.24510.02980.2192-28.292317.137618.1512
112.0493-0.50490.19952.0025-0.42821.2222-0.113-0.0372-0.2838-0.30580.0163-0.18910.3110.08810.05220.255-0.0282-0.03160.2033-0.00710.2271-25.53555.380121.9212
122.4654-0.2908-1.05721.7052-0.51373.5164-0.1464-0.8004-0.65030.20250.0456-0.07450.2120.58390.08350.3506-0.0033-0.0190.52740.16620.4338-29.8403-4.609737.2255
134.18960.45910.64444.88920.76833.76010.0966-0.1918-0.2046-0.2192-0.16450.43970.1308-0.27460.070.2524-0.0346-0.07160.30640.05660.2713-38.13562.508330.7327
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 100 )A71 - 100
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 180 )A101 - 180
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 213 )A181 - 213
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 260 )A214 - 260
7X-RAY DIFFRACTION7chain 'A' and (resid 261 through 306 )A261 - 306
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 43 )B1 - 43
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 100 )B44 - 100
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 180 )B101 - 180
11X-RAY DIFFRACTION11chain 'B' and (resid 181 through 213 )B181 - 213
12X-RAY DIFFRACTION12chain 'B' and (resid 214 through 274 )B214 - 274
13X-RAY DIFFRACTION13chain 'B' and (resid 275 through 302 )B275 - 302

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