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- PDB-7e6r: Crystal structure of HCoV-NL63 3C-like protease,pH5.6 -

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Basic information

Entry
Database: PDB / ID: 7e6r
TitleCrystal structure of HCoV-NL63 3C-like protease,pH5.6
Components3C-like proteinase
KeywordsVIRAL PROTEIN / HCoV-NL63 3C-like protease
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
Replicase polyprotein 1a
Similarity search - Component
Biological speciesHuman coronavirus NL63
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGao, H.X. / Zhang, Y.T. / Zhong, F.L. / Zhou, X.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 23, 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
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-11 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.136, 82.902, 63.902
Angle α, β, γ (deg.)90.000, 108.713, 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.: 282 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium citrate, pH5.6, 2% Tacsimate(pH5.0), 16% PEG3350

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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: 1.9→60.52 Å / Num. obs: 49375 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 26.2894691852 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.5
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 3558 / CC1/2: 0.398

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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: 7E6L

7e6l


Resolution: 1.9→60.52 Å / SU ML: 0.176280457739 / Cross valid method: NONE / σ(F): 1.33722732222 / Phase error: 22.182686881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222442851865 2377 4.82551411925 %
Rwork0.18696736093 46882 -
obs0.188700271271 49259 99.3946609092 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.908798125 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 0 282 4746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006508373308214566
X-RAY DIFFRACTIONf_angle_d0.8801524776426217
X-RAY DIFFRACTIONf_chiral_restr0.0566038874711711
X-RAY DIFFRACTIONf_plane_restr0.00522081796998798
X-RAY DIFFRACTIONf_dihedral_angle_d3.322576863472603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9340.3416517653111360.2941352771842666X-RAY DIFFRACTION96.0246744345
1.934-1.97610.2823095013941360.2312935835982755X-RAY DIFFRACTION99.6209510682
1.9761-2.02210.2359995883161460.1965836481862731X-RAY DIFFRACTION100
2.0221-2.07260.2428986777531400.1905945301032750X-RAY DIFFRACTION99.9654098928
2.0726-2.12870.241357328941470.17920060162777X-RAY DIFFRACTION100
2.1287-2.19130.2282161452471300.1898523317212771X-RAY DIFFRACTION100
2.1913-2.2620.2633945693421350.227905239642715X-RAY DIFFRACTION98.3436853002
2.262-2.34290.2411508314911560.1979570303482694X-RAY DIFFRACTION97.9381443299
2.3429-2.43670.2687186710251390.1999519661982764X-RAY DIFFRACTION100
2.4367-2.54760.2149157456571260.1979381774882781X-RAY DIFFRACTION99.9656121045
2.5476-2.68190.2530877041891430.2045763902582765X-RAY DIFFRACTION99.9656239257
2.6819-2.84990.2706581797441310.2057903370932790X-RAY DIFFRACTION100
2.8499-3.070.2480621137231240.2049361165342802X-RAY DIFFRACTION99.9658353263
3.07-3.37890.2258520148121540.1979731097292777X-RAY DIFFRACTION100
3.3789-3.86780.2103558010131470.1744570252442758X-RAY DIFFRACTION100
3.8678-4.87270.2020979419881510.1521270415682795X-RAY DIFFRACTION100
4.8727-60.520.1544177801571360.1617135712522791X-RAY DIFFRACTION97.9912956143

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