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- PDB-8im6: Crystal structure of HCoV 229E main protease in complex with PF07... -

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Basic information

Entry
Database: PDB / ID: 8im6
TitleCrystal structure of HCoV 229E main protease in complex with PF07304814
Components3C-like proteinase
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / mRNA guanylyltransferase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / mRNA guanylyltransferase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / 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 / RNA helicase activity / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus ...Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / 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 / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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
Similarity search - Domain/homology
Chem-80I / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHuman coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsZhou, Y.R. / Zeng, P. / Zhang, J. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural basis of main proteases of HCoV-229E bound to inhibitor PF-07304814 and PF-07321332.
Authors: Zhou, Y. / Wang, W. / Zeng, P. / Feng, J. / Li, D. / Jing, Y. / Zhang, J. / Yin, X. / Li, J. / Ye, H. / Wang, Q.
History
DepositionMar 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 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
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6474
Polymers65,5422
Non-polymers1,1052
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-10 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.522, 77.012, 74.626
Angle α, β, γ (deg.)90.000, 101.959, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / M-PRO / nsp5 / p34


Mass: 32771.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0C6X1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-80I / [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate


Mass: 552.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H33N4O9P / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus, protease inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 6000, 10% DMSO, 14% MPD, 0.1M Tris-HCL, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.01→52.98 Å / Num. obs: 39222 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.5587485405 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 9
Reflection shellResolution: 2.01→2.12 Å / Rmerge(I) obs: 0.779 / Num. unique obs: 5675

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→38.9 Å / SU ML: 0.243977159279 / Cross valid method: FREE R-VALUE / σ(F): 1.33542003918 / Phase error: 25.5830696087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.240283115588 3810 5.10758093706 %
Rwork0.204234258013 70785 -
obs0.206109610349 39188 96.7823548492 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.2619131164 Å2
Refinement stepCycle: LAST / Resolution: 2.01→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4417 0 76 151 4644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007079749074334599
X-RAY DIFFRACTIONf_angle_d0.8584644593246254
X-RAY DIFFRACTIONf_chiral_restr0.0552909215813690
X-RAY DIFFRACTIONf_plane_restr0.00503907900634807
X-RAY DIFFRACTIONf_dihedral_angle_d5.855791211232569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0145-2.040.3431601414521410.3157652335282586X-RAY DIFFRACTION95.3830010493
2.04-2.06680.3258478975451390.2889456623342592X-RAY DIFFRACTION96.8439716312
2.0668-2.09520.3109548871861440.2695420071172630X-RAY DIFFRACTION96.7561911406
2.0952-2.12510.2846483677091430.2650934632622644X-RAY DIFFRACTION96.6366158114
2.1251-2.15680.286914991141360.2634368609532520X-RAY DIFFRACTION94.6543121882
2.1568-2.19050.2856148419081370.2554788211452565X-RAY DIFFRACTION93.3333333333
2.1905-2.22640.2628159059531440.2536202682322599X-RAY DIFFRACTION95.7751396648
2.2264-2.26480.2499619691771370.2400013175352617X-RAY DIFFRACTION98.3571428571
2.2648-2.3060.2980842583541420.2440515432042688X-RAY DIFFRACTION98.3321751216
2.306-2.35030.3241690623181400.2384918430272675X-RAY DIFFRACTION98.2547993019
2.3503-2.39830.3195571073691420.2448440377542673X-RAY DIFFRACTION98.1862574119
2.3983-2.45040.3032646960881420.2402998177862637X-RAY DIFFRACTION97.8521126761
2.4504-2.50740.3116138828781430.2274696048772668X-RAY DIFFRACTION98.355493352
2.5074-2.57010.262435824441420.2230828288852652X-RAY DIFFRACTION97.7948897445
2.5701-2.63960.2625385982021400.216092989172627X-RAY DIFFRACTION97.5326048643
2.6396-2.71720.310372190261380.2196375943822632X-RAY DIFFRACTION97.5008799718
2.7172-2.80490.2407530920951470.2198934569262686X-RAY DIFFRACTION97.9598893499
2.8049-2.90510.2511934901351440.2061095312352591X-RAY DIFFRACTION97.4002849003
2.9051-3.02140.2402168555481400.2044594077372638X-RAY DIFFRACTION96.828163123
3.0214-3.15890.2126604353121420.2016353253932666X-RAY DIFFRACTION97.1962616822
3.1589-3.32530.2279614760391370.1979745674312602X-RAY DIFFRACTION96.2403373155
3.3253-3.53350.2259918286211380.1894504074792543X-RAY DIFFRACTION94.668079096
3.5335-3.80620.2136474926731430.1826960636382620X-RAY DIFFRACTION96.5408805031
3.8062-4.18880.2198659213721380.1684761417252569X-RAY DIFFRACTION95.4850088183
4.1888-4.7940.1606982792831430.152515217832605X-RAY DIFFRACTION95.7491289199
4.794-6.03630.2049473756161440.1790555029312633X-RAY DIFFRACTION97.1658502449
6.0363-38.90.2181486136261440.1762694183312627X-RAY DIFFRACTION96.8881118881

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