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- PDB-8zcc: Crystal structure of HCoV-NL63 main protease with X77 -

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Basic information

Entry
Database: PDB / ID: 8zcc
TitleCrystal structure of HCoV-NL63 main protease with X77
ComponentsHCoV-NL63 main protease
KeywordsVIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR COMPLEX
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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 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 / Pectin lyase fold/virulence factor / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus ...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 / Pectin lyase fold/virulence factor / 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
Similarity search - Domain/homology
Chem-X77 / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHuman coronavirus NL63
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsXu, J. / Li, W.W. / Yin, X.S. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of HCoV-NL63 main protease with X77
Authors: Xu, J. / Li, W.W. / Yin, X.S. / Li, J.
History
DepositionApr 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HCoV-NL63 main protease
B: HCoV-NL63 main protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5604
Polymers64,6412
Non-polymers9192
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-12 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.852, 82.235, 64.136
Angle α, β, γ (deg.)90.000, 108.416, 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 HCoV-NL63 main protease / 3CL-PRO / 3CLp / M-PRO / nsp5 / p34


Mass: 32320.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus NL63 / Gene: rep, 1a-1b / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P0C6X5, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-X77 / N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide


Mass: 459.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate tribasic dihydrate, 16% w/v Polyethylene glycol 3350, pH5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.978951 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978951 Å / Relative weight: 1
ReflectionResolution: 1.55→51.49 Å / Num. obs: 89859 / % possible obs: 99.5 % / Redundancy: 5 % / Biso Wilson estimate: 17.4006910356 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.4
Reflection shellResolution: 1.55→1.63 Å / Rmerge(I) obs: 1.43 / Num. unique obs: 13113

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→37.13 Å / SU ML: 0.183027823512 / Cross valid method: FREE R-VALUE / σ(F): 1.33752171184 / Phase error: 22.9157839014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213568081262 4283 4.81869423849 %
Rwork0.192660497265 84600 -
obs0.193663496262 88883 98.327341114 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.5262203244 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 68 375 4899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005994414454724632
X-RAY DIFFRACTIONf_angle_d0.8593596673536310
X-RAY DIFFRACTIONf_chiral_restr0.0608796257297714
X-RAY DIFFRACTIONf_plane_restr0.00545004687547806
X-RAY DIFFRACTIONf_dihedral_angle_d6.398106088522614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56350.304654683551320.2815338550932454X-RAY DIFFRACTION85.4311199207
1.5635-1.58190.3510438609061420.2772096119762644X-RAY DIFFRACTION92.7738927739
1.5819-1.60120.299206987571420.2779268271862657X-RAY DIFFRACTION94.7208121827
1.6012-1.62140.3053279697761510.2631753193332757X-RAY DIFFRACTION97.5184439973
1.6214-1.64280.2615818323371440.2566342836052866X-RAY DIFFRACTION98.8830486202
1.6428-1.66530.2994483925761580.2435304324722778X-RAY DIFFRACTION99.2227103751
1.6653-1.6890.2409765038631490.2336489550682888X-RAY DIFFRACTION99.6718083361
1.689-1.71430.2622881736771370.226854603432832X-RAY DIFFRACTION99.6643168849
1.7143-1.7410.2625345488681640.2338729833582836X-RAY DIFFRACTION99.8336106489
1.741-1.76960.2906684587261610.2278461737082831X-RAY DIFFRACTION99.7998665777
1.7696-1.80010.2476180209431370.2174196971512861X-RAY DIFFRACTION99.8667554963
1.8001-1.83280.2515407068761520.2235871955322838X-RAY DIFFRACTION99.3355481728
1.8328-1.86810.2222130371891250.2083019795372848X-RAY DIFFRACTION99.6313672922
1.8681-1.90620.252025028311340.2042111235412896X-RAY DIFFRACTION99.6055226824
1.9062-1.94770.2491824082321250.2002290495272863X-RAY DIFFRACTION99.566811063
1.9477-1.9930.2238372128241410.1982598560682777X-RAY DIFFRACTION97.6246236199
1.993-2.04280.2250643182581440.1942038015662861X-RAY DIFFRACTION99.8338870432
2.0428-2.0980.2259863114671380.1992652367632891X-RAY DIFFRACTION99.901055409
2.098-2.15980.212892885471510.1929461983462844X-RAY DIFFRACTION100
2.1598-2.22950.195071652161390.1984897229572855X-RAY DIFFRACTION99.7335109927
2.2295-2.30910.2248798685361600.1990952586532856X-RAY DIFFRACTION99.6036988111
2.3091-2.40160.2343048988721500.2027368960852861X-RAY DIFFRACTION99.7350115932
2.4016-2.51090.2210002113291450.2052372985312835X-RAY DIFFRACTION99.7322623829
2.5109-2.64320.2254581112471490.2059482976352877X-RAY DIFFRACTION99.637800461
2.6432-2.80870.2255523391811170.2040705766692872X-RAY DIFFRACTION99.3683510638
2.8087-3.02550.2160117492211120.1941522712362876X-RAY DIFFRACTION98.5163204748
3.0255-3.32980.1856288019471560.1885269378312797X-RAY DIFFRACTION97.5553353155
3.3298-3.81120.2036084635921460.1696046770232847X-RAY DIFFRACTION98.5187623436
3.8112-4.80010.1451403475161440.1476777084552832X-RAY DIFFRACTION97.8303747535
4.8001-37.130.1768362810951380.1563938975812870X-RAY DIFFRACTION96.8448164842

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