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- PDB-9kzf: PEDV 3CLpro mutant (C144A) in complex with nsp7/8 peptite substrate -

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Basic information

Entry
Database: PDB / ID: 9kzf
TitlePEDV 3CLpro mutant (C144A) in complex with nsp7/8 peptite substrate
Components
  • ORF1ab polyprotein
  • Replicase polyprotein 1a
KeywordsVIRAL PROTEIN / Coronavirus / PEDV / nsp5 / Mpro / 3CLpro / protein complex
Function / homology
Function and homology information


host cell membrane / viral genome replication / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 / methyltransferase cap1 activity ...host cell membrane / viral genome replication / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 / methyltransferase cap1 activity / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / lyase activity / viral protein processing / host cell perinuclear region of cytoplasm / symbiont-mediated activation of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / RNA-directed 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 / Pectin lyase fold/virulence factor / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus ...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 / Pectin lyase fold/virulence factor / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / 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 / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / 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 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
Similarity search - Domain/homology
Biological speciesPorcine epidemic diarrhea virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsZhang, Y. / Zhang, D. / Shi, Y.J. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: PEDV 3CLpro mutant (C144A) in complex with nsp7/8 peptite substrate
Authors: Zhang, Y. / Zhang, D. / Shi, Y.J. / Peng, G.Q.
History
DepositionDec 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF1ab polyprotein
B: ORF1ab polyprotein
C: Replicase polyprotein 1a
D: Replicase polyprotein 1a


Theoretical massNumber of molelcules
Total (without water)69,3084
Polymers69,3084
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-24 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.005, 91.413, 58.099
Angle α, β, γ (deg.)90.00, 100.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ORF1ab polyprotein


Mass: 33947.352 Da / Num. of mol.: 2 / Mutation: C144A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine epidemic diarrhea virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023J7B5
#2: Protein/peptide Replicase polyprotein 1a


Mass: 706.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Porcine epidemic diarrhea virus
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.05M Citric acid,0.05M BIS-TRIS(propane/PH5.0),16%w/v Polyethyleneglycol3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→57.16 Å / Num. obs: 55994 / % possible obs: 99.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.8
Reflection shellResolution: 1.78→1.87 Å / Rmerge(I) obs: 1.483 / Num. unique obs: 7917

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→28.69 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 2796 5.07 %
Rwork0.2027 --
obs0.2034 55148 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 0 248 4854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0244696
X-RAY DIFFRACTIONf_angle_d1.3496372
X-RAY DIFFRACTIONf_dihedral_angle_d15.9171634
X-RAY DIFFRACTIONf_chiral_restr0.09722
X-RAY DIFFRACTIONf_plane_restr0.011818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.810.35621110.32092100X-RAY DIFFRACTION79
1.81-1.840.31531610.30622347X-RAY DIFFRACTION89
1.84-1.870.32421550.30872490X-RAY DIFFRACTION94
1.87-1.910.31951430.29052555X-RAY DIFFRACTION97
1.91-1.950.26391460.26292635X-RAY DIFFRACTION98
1.95-20.27061550.26022614X-RAY DIFFRACTION98
2-2.050.31721410.25472647X-RAY DIFFRACTION99
2.05-2.10.2951270.24482669X-RAY DIFFRACTION99
2.1-2.170.25421200.23562660X-RAY DIFFRACTION99
2.17-2.240.25161290.23512690X-RAY DIFFRACTION100
2.24-2.320.23481190.22062693X-RAY DIFFRACTION100
2.32-2.410.23021630.22232646X-RAY DIFFRACTION100
2.41-2.520.23581420.23462694X-RAY DIFFRACTION100
2.52-2.650.2591420.22872673X-RAY DIFFRACTION100
2.65-2.820.24041600.22432657X-RAY DIFFRACTION100
2.82-3.030.1951420.19072706X-RAY DIFFRACTION100
3.03-3.340.19361390.19312696X-RAY DIFFRACTION100
3.34-3.820.18811480.17472687X-RAY DIFFRACTION100
3.82-4.810.16581280.14492719X-RAY DIFFRACTION100
4.81-8.690.14331250.13822774X-RAY DIFFRACTION100

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