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- PDB-7e6l: Crystal structure of HCoV-NL63 3C-like protease,pH5.0 -

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Basic information

Entry
Database: PDB / ID: 7e6l
TitleCrystal structure of HCoV-NL63 3C-like protease,pH5.0
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 / host cell perinuclear region of cytoplasm / viral protein processing / 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
Replicase polyprotein 1a
Similarity search - Component
Biological speciesHuman coronavirus NL63
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78037145659 Å
AuthorsGao, H.X. / Zhang, Y.T. / Zhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structures of human coronavirus NL63 main protease at different pH values
Authors: Gao, H. / Zhang, Y. / Jiang, H. / Hu, X. / Zhang, Y. / Zhou, X. / Zhong, F. / Lin, C. / Li, J. / Luo, J. / Zhang, J.
History
DepositionFeb 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: 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


Theoretical massNumber of molelcules
Total (without water)65,5262
Polymers65,5262
Non-polymers00
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-9 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.070, 82.400, 63.920
Angle α, β, γ (deg.)90.000, 108.466, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion
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: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→60.63 Å / Num. obs: 59245 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.0525518452 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.9
Reflection shellResolution: 1.78→1.83 Å / Rmerge(I) obs: 0.173 / Num. unique obs: 4319

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TLO

3tlo


Resolution: 1.78037145659→59.8563 Å / SU ML: 0.166231757271 / Cross valid method: NONE / σ(F): 1.38328402385 / Phase error: 19.4674936868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201607044392 3034 5.12707854536 %
Rwork0.181035795676 56142 -
obs0.182118735201 59176 99.5826602046 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8386610369 Å2
Refinement stepCycle: LAST / Resolution: 1.78037145659→59.8563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4491 0 0 348 4839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006175939554784593
X-RAY DIFFRACTIONf_angle_d0.8312567011236249
X-RAY DIFFRACTIONf_chiral_restr0.0561034761985713
X-RAY DIFFRACTIONf_plane_restr0.00503876879582801
X-RAY DIFFRACTIONf_dihedral_angle_d3.18543160822625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7804-1.80820.2345347441631390.2151496996822497X-RAY DIFFRACTION97.8470675575
1.8082-1.83780.2186346958651540.2017679891422499X-RAY DIFFRACTION99.1034740381
1.8378-1.86950.2193005717461390.1870500340842527X-RAY DIFFRACTION99.3663809169
1.8695-1.90350.213460695581500.1849467511642539X-RAY DIFFRACTION99.5557201037
1.9035-1.94010.2019441968721420.1851492600972531X-RAY DIFFRACTION99.6272828923
1.9401-1.97970.2415848586981630.1845537641612518X-RAY DIFFRACTION99.5174461767
1.9797-2.02280.2136579643461170.177154242462557X-RAY DIFFRACTION99.6274217586
2.0228-2.06990.2213593770751110.185889015182578X-RAY DIFFRACTION99.7773654917
2.0699-2.12160.2117549945121380.1848332280492565X-RAY DIFFRACTION99.8522349464
2.1216-2.1790.2452813852771210.182385394872571X-RAY DIFFRACTION99.8886827458
2.179-2.24310.2253207348451490.189350773382535X-RAY DIFFRACTION99.9255398362
2.2431-2.31550.223558812231110.1877103445742589X-RAY DIFFRACTION99.925980755
2.3155-2.39830.2055278517751170.1959305191912557X-RAY DIFFRACTION100
2.3983-2.49430.1936239367641330.1925642103552563X-RAY DIFFRACTION100
2.4943-2.60780.2306069264881180.1987986989742575X-RAY DIFFRACTION99.9628804751
2.6078-2.74530.1933407997351530.201890613952584X-RAY DIFFRACTION99.9634769905
2.7453-2.91730.2011085619221580.19151188972512X-RAY DIFFRACTION100
2.9173-3.14250.2013247317091670.1898005064382550X-RAY DIFFRACTION99.9632082414
3.1425-3.45880.2107873887761300.1858940063832577X-RAY DIFFRACTION100
3.4588-3.95920.2046198726361200.1619729400162609X-RAY DIFFRACTION99.9633699634
3.9592-4.98770.1698537228541570.1573101012442560X-RAY DIFFRACTION99.9632082414
4.9877-59.82254315120.1833462144961470.1749616720582549X-RAY DIFFRACTION97.1181556196

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