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- PDB-4xfq: Crystal Structure Basis for PEDV 3C Like Protease -

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Basic information

Entry
Database: PDB / ID: 4xfq
TitleCrystal Structure Basis for PEDV 3C Like Protease
ComponentsPEDV main protease
KeywordsHYDROLASE / Porcine epidemic diarrhea virus / 3C-Like Protease
Function / homology
Function and homology information


host cell membrane / viral genome replication / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity ...host cell membrane / viral genome replication / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / virus-mediated perturbation of host defense response / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / 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 / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Pectin lyase fold/virulence factor ...: / 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 / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Pectin lyase fold/virulence factor / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / : / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / 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 3Ecto domain profile. / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Trypsin-like serine proteases / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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
Similarity search - Domain/homology
Biological speciesPorcine epidemic diarrhea virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsYe, G. / Fu, Z.F. / Peng, G.Q.
CitationJournal: Virology / Year: 2016
Title: Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease.
Authors: Ye, G. / Deng, F. / Shen, Z. / Luo, R. / Zhao, L. / Xiao, S. / Fu, Z.F. / Peng, G.
History
DepositionDec 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine / software
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_method_to_determine_struct / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEDV main protease
B: PEDV main protease


Theoretical massNumber of molelcules
Total (without water)66,5912
Polymers66,5912
Non-polymers00
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-12 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.644, 91.058, 57.984
Angle α, β, γ (deg.)90.000, 100.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PEDV main protease


Mass: 33295.641 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2998-3295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine epidemic diarrhea virus / Gene: Pol1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: K4L9I6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 5% PEG3350, 0.1M NaCl, 0.2M Na2HPO4:Citric Acid pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 69155 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Χ2: 1.234 / Net I/av σ(I): 23.249 / Net I/σ(I): 13 / Num. measured all: 257484
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.713.70.4869230.8790.2890.5611.24299.9
1.71-1.783.70.35168680.9290.2110.411.29899.9
1.78-1.863.70.2469230.960.1440.281.29699.9
1.86-1.963.70.15668880.9810.0940.1831.31299.9
1.96-2.083.80.10769120.9910.0640.1251.29299.9
2.08-2.243.80.07669180.9950.0460.0891.22899.8
2.24-2.463.80.06469160.9960.0380.0741.07799.9
2.46-2.823.70.06369320.9940.0380.0741.35699.9
2.82-3.553.60.04769470.9970.0280.0551.19199.8
3.55-503.70.03269280.9980.0190.0381.0598.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data processing
PHENIX1.8.2-1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9S

1p9s


Resolution: 1.65→27.454 Å / FOM work R set: 0.849 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 2005 2.9 %
Rwork0.1777 67105 -
obs0.1786 69110 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.42 Å2 / Biso mean: 24.85 Å2 / Biso min: 10.22 Å2
Refinement stepCycle: final / Resolution: 1.65→27.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 0 461 4975
Biso mean---34.02 -
Num. residues----592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074605
X-RAY DIFFRACTIONf_angle_d1.1376251
X-RAY DIFFRACTIONf_chiral_restr0.078706
X-RAY DIFFRACTIONf_plane_restr0.004803
X-RAY DIFFRACTIONf_dihedral_angle_d13.9491607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6505-1.69170.28351330.24214639477296
1.6917-1.73750.23411430.223147654908100
1.7375-1.78860.24941440.207448074951100
1.7886-1.84630.24741470.209847674914100
1.8463-1.91230.2471420.190948294971100
1.9123-1.98880.25851400.183748204960100
1.9888-2.07930.20471460.180447834929100
2.0793-2.18890.17871470.176547964943100
2.1889-2.3260.22071460.17847944940100
2.326-2.50540.20051410.181448174958100
2.5054-2.75740.21811440.19148314975100
2.7574-3.15580.2111490.183248274976100
3.1558-3.97410.19581390.161448034942100
3.9741-27.45810.16671440.15824827497198

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