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- PDB-9uop: Crystal structure of CCoV-HuPn-2018 3CL protease (3CLpro) in comp... -

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Basic information

Entry
Database: PDB / ID: 9uop
TitleCrystal structure of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with compound 8
Components3C-like protease
KeywordsVIRAL PROTEIN / Mpro / VIRAL PROTEIN-inhibitor complex
Function / homology
Function and homology information


host cell membrane / viral genome replication / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity ...host cell membrane / viral genome replication / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / viral protein processing / lyase activity / host cell perinuclear region of cytoplasm / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / 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 / NSP15, NendoU domain, coronavirus ...Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / 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 / 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. / 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
Similarity search - Domain/homology
: / ORF1ab polyprotein
Similarity search - Component
Biological speciesCanine coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsNie, T.Q. / Su, H.X. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci / Year: 2025
Title: Structure-Based Development of Ultra-Broad-Spectrum 3C-Like Protease Inhibitors.
Authors: Su, H. / Nie, T. / Chen, G. / Xiong, M. / Zhang, Y. / Wu, G. / You, M. / Xie, H. / He, J. / Xiong, Y. / Hu, H. / Zhao, W. / Li, M. / Xiao, G. / Zhang, L. / Xu, Y.
History
DepositionApr 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 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: 3C-like protease
B: 3C-like protease
C: 3C-like protease
D: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0638
Polymers132,1494
Non-polymers1,9144
Water14,376798
1
A: 3C-like protease
C: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0324
Polymers66,0752
Non-polymers9572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-12 kcal/mol
Surface area24940 Å2
MethodPISA
2
B: 3C-like protease
hetero molecules

D: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0324
Polymers66,0752
Non-polymers9572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area2690 Å2
ΔGint-14 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.260, 127.530, 111.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-626-

HOH

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Components

#1: Protein
3C-like protease


Mass: 33037.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine coronavirus 2 / Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A8F2ZG71
#2: Chemical
ChemComp-A1EPZ / (2~{S})-2-[[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]amino]-4-methyl-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]pentanamide


Type: peptide-like / Mass: 478.506 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H33F3N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG3350, 200 mM Lithium citrate tribasic tetrahydrate, pH8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.61→111.2 Å / Num. obs: 206456 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.044 / Rrim(I) all: 0.16 / Χ2: 0.85 / Net I/σ(I): 11.1 / Num. measured all: 2763943
Reflection shellResolution: 1.61→1.7 Å / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 4.036 / Num. measured all: 385437 / Num. unique obs: 29886 / CC1/2: 0.458 / Rpim(I) all: 1.164 / Rrim(I) all: 4.205 / Χ2: 0.73 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→22.2 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 10207 4.99 %
Rwork0.2005 --
obs0.202 204510 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→22.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9119 0 132 798 10049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149563
X-RAY DIFFRACTIONf_angle_d1.26312981
X-RAY DIFFRACTIONf_dihedral_angle_d7.2621437
X-RAY DIFFRACTIONf_chiral_restr0.0811465
X-RAY DIFFRACTIONf_plane_restr0.0091661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.40212960.38395660X-RAY DIFFRACTION87
1.63-1.650.39043440.37716021X-RAY DIFFRACTION94
1.65-1.670.34822840.35546349X-RAY DIFFRACTION97
1.67-1.690.38493350.33796362X-RAY DIFFRACTION99
1.69-1.710.34943190.32736450X-RAY DIFFRACTION99
1.71-1.730.33793330.31016493X-RAY DIFFRACTION100
1.73-1.760.34543700.29096419X-RAY DIFFRACTION100
1.76-1.780.28263490.28176456X-RAY DIFFRACTION100
1.78-1.810.33573950.27126420X-RAY DIFFRACTION100
1.81-1.840.29243460.25666480X-RAY DIFFRACTION100
1.84-1.870.28614060.24236423X-RAY DIFFRACTION100
1.87-1.910.25963130.23476510X-RAY DIFFRACTION100
1.91-1.940.26693000.22566534X-RAY DIFFRACTION100
1.94-1.980.24353390.21436471X-RAY DIFFRACTION100
1.98-2.030.2583480.21356521X-RAY DIFFRACTION100
2.03-2.070.24863670.20976458X-RAY DIFFRACTION100
2.07-2.130.26233510.2046493X-RAY DIFFRACTION100
2.13-2.180.24283630.20126486X-RAY DIFFRACTION100
2.18-2.250.25943320.20196514X-RAY DIFFRACTION100
2.25-2.320.25543130.20316565X-RAY DIFFRACTION100
2.32-2.40.22753350.20196524X-RAY DIFFRACTION100
2.4-2.50.23883560.20556547X-RAY DIFFRACTION100
2.5-2.610.23963520.20046525X-RAY DIFFRACTION100
2.61-2.750.22233390.20146557X-RAY DIFFRACTION100
2.75-2.920.24743190.20166585X-RAY DIFFRACTION100
2.92-3.150.23543260.20126598X-RAY DIFFRACTION100
3.15-3.460.21463620.19326586X-RAY DIFFRACTION100
3.46-3.960.20133080.17116693X-RAY DIFFRACTION100
3.96-4.980.14563380.14026703X-RAY DIFFRACTION100
4.98-22.20.17383690.16336900X-RAY DIFFRACTION100

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