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- PDB-8p5b: Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-... -

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Basic information

Entry
Database: PDB / ID: 8p5b
TitleCrystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 obtained in presence of 500 micromolar X77 enantiomer S.
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Mpro / 3CLpro / EXSCALATE4COV / drug discovery / Elettra
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase 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 toll-like receptor signaling pathway / 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 / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase 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 / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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 / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / 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 / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) 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 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.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsCostanzi, E. / Demitri, N. / Storici, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101003551European Union
CitationJournal: J.Chem.Inf.Model. / Year: 2024
Title: Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease.
Authors: Albani, S. / Costanzi, E. / Hoang, G.L. / Kuzikov, M. / Frings, M. / Ansari, N. / Demitri, N. / Nguyen, T.T. / Rizzi, V. / Schulz, J.B. / Bolm, C. / Zaliani, A. / Carloni, P. / Storici, P. / Rossetti, G.
History
DepositionMay 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: 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 nsp5
B: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9908
Polymers67,6512
Non-polymers3396
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-22 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.930, 99.831, 103.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3C-like proteinase nsp5 / 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
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase

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Non-polymers , 5 types, 683 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium formate 0.1M Ammonium acetate 0.1M Sodium citrate tribasic dihydrate 0.1M Potassium sodium tartrate tetrahydrate 0.1M Sodium oxamate, 0.1M imidazole/MES pH 6.5, 12.5% v/v MPD 12. ...Details: 0.1 M Sodium formate 0.1M Ammonium acetate 0.1M Sodium citrate tribasic dihydrate 0.1M Potassium sodium tartrate tetrahydrate 0.1M Sodium oxamate, 0.1M imidazole/MES pH 6.5, 12.5% v/v MPD 12.5% PEG 1000 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.47→103.72 Å / Num. obs: 121551 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.9
Reflection shellResolution: 1.47→1.49 Å / Num. unique obs: 5949 / CC1/2: 0.664

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BB2

7bb2


Resolution: 1.47→51.86 Å / SU ML: 0.1502 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.0074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.178 5993 4.94 %
Rwork0.1644 115372 -
obs0.1651 121365 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.39 Å2
Refinement stepCycle: LAST / Resolution: 1.47→51.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 18 677 5421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634868
X-RAY DIFFRACTIONf_angle_d0.93326615
X-RAY DIFFRACTIONf_chiral_restr0.0749744
X-RAY DIFFRACTIONf_plane_restr0.0076862
X-RAY DIFFRACTIONf_dihedral_angle_d13.74041738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.480.331840.31823795X-RAY DIFFRACTION99.87
1.48-1.50.30242000.26373815X-RAY DIFFRACTION99.9
1.5-1.520.30262030.27023769X-RAY DIFFRACTION99.2
1.52-1.540.29172130.2933779X-RAY DIFFRACTION99.43
1.54-1.560.24032030.23133795X-RAY DIFFRACTION99.97
1.56-1.580.24842030.21613819X-RAY DIFFRACTION100
1.58-1.60.2251880.21363809X-RAY DIFFRACTION100
1.6-1.620.23952080.21173825X-RAY DIFFRACTION100
1.62-1.650.20872110.20613785X-RAY DIFFRACTION100
1.65-1.680.24661970.19133854X-RAY DIFFRACTION100
1.68-1.710.17961900.18553801X-RAY DIFFRACTION99.92
1.71-1.740.20632030.18593811X-RAY DIFFRACTION99.98
1.74-1.770.19221860.17483836X-RAY DIFFRACTION100
1.77-1.810.19082220.17093790X-RAY DIFFRACTION99.98
1.81-1.850.20172390.17473791X-RAY DIFFRACTION99.98
1.85-1.890.18511970.18533846X-RAY DIFFRACTION99.98
1.89-1.940.20652130.18743795X-RAY DIFFRACTION99.75
1.94-1.990.18851780.16863853X-RAY DIFFRACTION99.98
1.99-2.050.19591960.16243842X-RAY DIFFRACTION99.98
2.05-2.110.18882060.16083843X-RAY DIFFRACTION99.83
2.11-2.190.21281930.15083848X-RAY DIFFRACTION100
2.19-2.280.17791910.15313874X-RAY DIFFRACTION99.98
2.28-2.380.16192010.15083833X-RAY DIFFRACTION99.95
2.38-2.510.17011700.15523895X-RAY DIFFRACTION99.98
2.51-2.660.18752040.15293878X-RAY DIFFRACTION99.98
2.66-2.870.1741880.15483901X-RAY DIFFRACTION99.83
2.87-3.160.18121950.15893887X-RAY DIFFRACTION99.83
3.16-3.610.14481730.14973958X-RAY DIFFRACTION99.83
3.61-4.550.13812070.13273953X-RAY DIFFRACTION99.74
4.55-51.860.15262310.16334092X-RAY DIFFRACTION99.52
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)
12.71724919383-0.0761036478117-0.4977304821010.787367249716-0.1144097907561.96322616591-0.0518008919155-0.08174479365540.03462510505770.0177907953593-0.00675021424865-0.004909164986660.001983665105640.1977782384670.06033570271290.1323422759370.0145428047088-0.001239091863650.1217517507590.0004447178680370.12086010693418.1502979461-7.22874783988-18.3065697375
22.504718796340.377751868189-1.335178335821.05408900202-1.119053924224.494254498550.0059090339729-0.257376793450.1428568876670.1541694803890.00351360913794-0.0337332284688-0.3476233919940.220849613571-0.007812750559830.20656018040.00308979501737-0.01119815830390.2958440996880.01835191113480.2267136287834.0715423663-3.399337535-24.4739739239
31.51132890173-0.2112351530160.1104609688360.785090498914-0.6065113773141.95132175332-0.0597853594628-0.0756815372756-0.2079960513440.0139828604374-0.081402760652-0.1157134994720.152739528380.3658867044330.1089866227740.1638795053380.05929711348120.02298088916570.1590544944490.01040439759290.18880496702221.9465616781-14.6967769613-22.8623986361
43.06969841701-0.1164494435920.5351740505341.013851306130.4553302110373.37585691777-0.01578177203540.02773019007810.0282369680094-0.00984865008577-0.0155377465107-0.00617232852843-0.0380520248930.08053041862540.04197362614850.1175144447880.00303365424760.002753465924970.1113586342070.006502898024940.14076905452511.3126986489-4.90092211286-23.0379131151
53.504320651510.319612263864-0.4955418853560.5445634568980.4452786288971.092780827260.008724647961650.519223860950.319744011374-0.09171248838520.0238693069393-0.0279323805447-0.1948550210160.0913318754628-0.02143353519550.171639022038-0.00120259008465-0.00597023543850.2313725777330.04215123050030.16368846722614.5302302287-1.43940090953-35.1045791142
61.71769044797-0.2358861736970.5236717004191.60013235985-0.2311704092192.43024468096-0.0174938593135-0.0925498399378-0.0680161355950.07928589284060.03340316195130.1123542317660.000261294569045-0.0805115199122-0.01530565545420.1242689809930.00218861886202-0.001354452652740.159134510605-1.22804404834E-50.163674374806-12.9595859544-7.49329543234-32.2425205833
71.44772236986-0.256170842205-0.11440231510.731109798794-0.4698806315232.47663052447-0.0272729246697-0.108405737257-0.167659896345-0.0278076501751-0.03300877635580.009766079612780.2777657505890.03654828109790.05394428918080.1885016570270.005589935649740.01224429876460.0954244103698-0.002288803630250.148601592398-0.0353155896773-10.7140822511-1.34163235443
82.03452256653-0.8823681215680.4948722027441.27651271018-0.264562065742.63557239693-0.0228807321654-0.232809349257-0.2091712936010.05726470926930.05729435666510.09035327735550.305241383119-0.1689582574060.02129216349960.167170052471-0.0236662327260.0254212443490.1198555533620.02744073766290.145241594757-4.79377043716-8.722965279361.90009525342
90.7898282700690.442559079597-0.6739003608161.92600697514-1.365271651192.724457547390.102601950281-0.006319661862640.13482176953-0.001315152143020.04249281760910.016989671999-0.3188593229410.013715979864-0.1287567240590.1838756162220.005433048486550.03246034423770.111027165585-0.01725936469490.165497905991-4.9569287999715.9966497181-14.3975878912
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )AA1 - 431 - 43
22chain 'A' and (resid 44 through 76 )AA44 - 7644 - 76
33chain 'A' and (resid 77 through 110 )AA77 - 11077 - 110
44chain 'A' and (resid 111 through 166 )AA111 - 166111 - 166
55chain 'A' and (resid 167 through 200 )AA167 - 200167 - 200
66chain 'A' and (resid 201 through 306 )AA201 - 306201 - 306
77chain 'B' and (resid 1 through 43 )BD1 - 431 - 43
88chain 'B' and (resid 44 through 180 )BD44 - 18044 - 180
99chain 'B' and (resid 181 through 305 )BD181 - 305181 - 305

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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