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- PDB-7eo7: Crystal structure of HCoV-NL63 3C-like protease in complex with a... -

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Basic information

Entry
Database: PDB / ID: 7eo7
TitleCrystal structure of HCoV-NL63 3C-like protease in complex with an inhibitor Shikonin
Components3C-like proteinase
KeywordsVIRAL PROTEIN / HCoV
Function / homology
Function and homology information


host cell membrane / viral genome replication / transferase 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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / regulation of autophagy ...host cell membrane / viral genome replication / transferase 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 / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / Pectin lyase fold/virulence factor / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal ...Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / Pectin lyase fold/virulence factor / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / 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 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Thrombin, subunit H / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-FNO / Replicase polyprotein 1a
Similarity search - Component
Biological speciesHuman coronavirus NL63
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24916621935 Å
AuthorsGao, H.X. / Zhang, Y.T. / Zhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2022
Title: Structure-Based Discovery and Structural Basis of a Novel Broad-Spectrum Natural Product against the Main Protease of Coronavirus.
Authors: Zhang, Y. / Gao, H. / Hu, X. / Wang, Q. / Zhong, F. / Zhou, X. / Lin, C. / Yang, Y. / Wei, J. / Du, W. / Huang, H. / Zhou, H. / He, W. / Zhang, H. / Zhang, Y. / McCormick, P.J. / Fu, J. / ...Authors: Zhang, Y. / Gao, H. / Hu, X. / Wang, Q. / Zhong, F. / Zhou, X. / Lin, C. / Yang, Y. / Wei, J. / Du, W. / Huang, H. / Zhou, H. / He, W. / Zhang, H. / Zhang, Y. / McCormick, P.J. / Fu, J. / Wang, D. / Fu, Y. / Lu, X. / Zhang, T. / Duan, J. / Qin, B. / Jiang, H. / Luo, J. / Zhang, Y. / Chen, Q. / Luo, Q. / Cheng, L. / Zhang, Z. / Zhang, J. / Li, J.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8153
Polymers65,5262
Non-polymers2881
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-10 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.282, 82.892, 64.097
Angle α, β, γ (deg.)90.000, 108.365, 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


Mass: 32763.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus NL63 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0C6U6, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-FNO / 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione / shikonin


Mass: 288.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
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: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.24916621935→51.6408506815 Å / Num. obs: 29768 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.2342051286 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.1
Reflection shellResolution: 2.25→2.31 Å / Rmerge(I) obs: 0.182 / Num. unique obs: 2086

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E6L

7e6l


Resolution: 2.24916621935→51.6408506815 Å / SU ML: 0.244127943788 / Cross valid method: FREE R-VALUE / σ(F): 1.45034303898 / Phase error: 22.585818759
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232149549676 1457 4.90242261104 %
Rwork0.176544080246 28263 -
obs0.179115181175 29720 99.2386803793 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.0004243652 Å2
Refinement stepCycle: LAST / Resolution: 2.24916621935→51.6408506815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 21 120 4619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007359847499654602
X-RAY DIFFRACTIONf_angle_d0.8518853422736266
X-RAY DIFFRACTIONf_chiral_restr0.0547330593842714
X-RAY DIFFRACTIONf_plane_restr0.00497322773096800
X-RAY DIFFRACTIONf_dihedral_angle_d3.28289134482618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2492-2.32960.2611306206831590.2014240408212716X-RAY DIFFRACTION96.4765100671
2.3296-2.42280.2374335462731470.1966767502672793X-RAY DIFFRACTION99.257258609
2.4228-2.53310.2828125042091570.1994948131642797X-RAY DIFFRACTION99.2607526882
2.5331-2.66660.3079231427381720.2092882223832812X-RAY DIFFRACTION99.5330220147
2.6666-2.83370.314157769921280.209141703662826X-RAY DIFFRACTION99.5618469835
2.8337-3.05250.2581937070981710.1987299576132813X-RAY DIFFRACTION99.665998664
3.0525-3.35960.2311561032141420.1894360496892843X-RAY DIFFRACTION99.7660427807
3.3596-3.84560.1842918726581340.1637204518762852X-RAY DIFFRACTION99.9330655957
3.8456-4.84450.2091981696831140.150209379842905X-RAY DIFFRACTION99.9668874172
4.8445-51.64085068150.2043669765511330.1652443308452906X-RAY DIFFRACTION99.0224828935

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