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- PDB-6noz: X-ray structure of PEDV papain-like protease 2 -

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Basic information

Entry
Database: PDB / ID: 6noz
TitleX-ray structure of PEDV papain-like protease 2
ComponentsPolyproteinProteolysis
KeywordsHYDROLASE / papain-like / viral protein / protease / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


exonuclease activity / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / viral genome replication / methyltransferase activity / methylation / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 ...exonuclease activity / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / viral genome replication / methyltransferase activity / methylation / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / RNA helicase activity / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Pectin lyase fold/virulence factor / 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 / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus ...Pectin lyase fold/virulence factor / 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 / 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. / 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 viral protease, palm and finger domains, coronavirus / 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 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 / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPorcine epidemic diarrhea virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsClasman, J.C. / Mesecar, A.D. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI085089 United States
CitationJournal: To Be Published
Title: Evaluating ubiquitin specificity of papain-like protease 2 from alphacoronaviruses FIPV and PEDV using structure-guided engineering
Authors: Clasman, J.C. / Mesecar, A.D.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4395
Polymers27,0981
Non-polymers3424
Water6,305350
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Oligomers of PEDV PLP2 form at high concentrations by SDS-PAGE analysis. PEDV PLP2 elutes in one single peak using size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint1 kcal/mol
Surface area12410 Å2
Unit cell
Length a, b, c (Å)49.722, 65.672, 170.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Polyprotein / Proteolysis


Mass: 27097.762 Da / Num. of mol.: 1 / Fragment: UNP Residues 1688-1933
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine epidemic diarrhea virus / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: W8QLX4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 1.3 M K/Na tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. obs: 20909 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 13.45 Å2 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.066 / Rrim(I) all: 0.177 / Χ2: 1.488 / Net I/σ(I): 6.4 / Num. measured all: 148740
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.9870.58110210.9130.2350.6271.179100
1.98-2.0270.5319910.9070.2150.5731.18100
2.02-2.0670.48510730.9390.1960.5231.209100
2.06-2.17.10.43510050.9310.1750.471.256100
2.1-2.157.20.40310410.9460.1610.4341.214100
2.15-2.27.10.36610290.9630.1470.3951.225100
2.2-2.257.20.33410240.9690.1330.361.239100
2.25-2.317.20.3310430.9680.1320.3561.218100
2.31-2.387.20.30110170.9660.120.3251.254100
2.38-2.467.20.27210450.9810.1080.2931.24100
2.46-2.547.20.24210440.9840.0970.2611.271100
2.54-2.657.30.21510310.9830.0860.2311.303100
2.65-2.777.20.18310600.9890.0730.1971.325100
2.77-2.917.30.16610420.9920.0660.1791.327100
2.91-3.17.20.13610280.9930.0540.1461.448100
3.1-3.337.20.12410510.9910.050.1341.957100
3.33-3.6770.10610580.9930.0440.1142.591100
3.67-4.26.90.09110730.9960.0380.0992.788100
4.2-5.297.20.06610770.9970.0270.0712.076100
5.29-1006.80.04911560.9990.020.0531.42199.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MP2

3mp2


Resolution: 1.95→35.928 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.79
RfactorNum. reflection% reflection
Rfree0.1931 1945 9.61 %
Rwork0.1447 --
obs0.1493 20248 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.17 Å2 / Biso mean: 16.7414 Å2 / Biso min: 3.58 Å2
Refinement stepCycle: final / Resolution: 1.95→35.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 19 357 2281
Biso mean--38.82 26.58 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072010
X-RAY DIFFRACTIONf_angle_d1.0252746
X-RAY DIFFRACTIONf_chiral_restr0.044312
X-RAY DIFFRACTIONf_plane_restr0.005354
X-RAY DIFFRACTIONf_dihedral_angle_d13.476698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9461-1.99480.2271300.16661213134392
1.9948-2.04870.22651350.16091262139794
2.0487-2.1090.21271330.15081252138596
2.109-2.17710.21291380.15571295143396
2.1771-2.25490.21071370.14811267140496
2.2549-2.34510.20411300.15031262139295
2.3451-2.45180.21321380.15321293143196
2.4518-2.58110.24321390.15051308144797
2.5811-2.74270.18951420.15791324146698
2.7427-2.95440.1951400.15261322146298
2.9544-3.25150.17811400.14941330147099
3.2515-3.72160.17441460.12551363150999
3.7216-4.68720.1411440.11561367151199
4.6872-35.93410.19681530.149714451598100

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