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- PDB-5zqg: Complex structure of PEDV 3CLpro mutant (C144A) with NEMO-231 pep... -

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Basic information

Entry
Database: PDB / ID: 5zqg
TitleComplex structure of PEDV 3CLpro mutant (C144A) with NEMO-231 peptite substrate
Components
  • Non-structural protein
  • PEPTIDE LEU-ALA-GLN-LEU-GLN-VAL-ALA
KeywordsHYDROLASE/PEPTIDE / 3C-like protease / complex structure / NEMO / PEDV 3CLpro / mutant / C144A / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


host cell membrane / viral genome replication / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase 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 / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase 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 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / lyase activity / viral protein processing / host cell perinuclear region of cytoplasm / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding
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 / Coronavirus replicase NSP2, C-terminal / main proteinase (3clpro) structure, domain 3 ...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 / Coronavirus replicase NSP2, C-terminal / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / 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 / Thrombin, subunit H / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / : / Coronavirus replicase NSP2, N-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 Nsp3 ectodomain (3Ecto) 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
Similarity search - Domain/homology
Biological speciesPorcine epidemic diarrhea virus
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGang, Y. / Chen, J.Y. / Dang, W. / Xiao, S.B. / Peng, G.Q.
CitationJournal: To Be Published
Title: Complex structure of PEDV 3CLpro mutant (C144A) with NEMO peptite substrate
Authors: Gang, Y. / Chen, J.Y.
History
DepositionApr 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein
B: Non-structural protein
C: PEPTIDE LEU-ALA-GLN-LEU-GLN-VAL-ALA


Theoretical massNumber of molelcules
Total (without water)68,5753
Polymers68,5753
Non-polymers00
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-20 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.576, 92.434, 58.029
Angle α, β, γ (deg.)90.00, 100.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Non-structural protein / 3CLpro


Mass: 33637.043 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: R4JK63
#2: Protein/peptide PEPTIDE LEU-ALA-GLN-LEU-GLN-VAL-ALA


Mass: 1300.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M NaCL, 0.2M Na2HPO4:citric acid (pH 4.2), 5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 83591 / % possible obs: 99 % / Redundancy: 6.2 % / Rpim(I) all: 0.023 / Net I/σ(I): 29.96
Reflection shellResolution: 1.6→1.66 Å / Rpim(I) all: 0.084

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFQ

4xfq


Resolution: 1.6→35.562 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2235 2008 2.62 %
Rwork0.1941 --
obs0.1949 76639 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→35.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 0 356 4880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074613
X-RAY DIFFRACTIONf_angle_d1.0966259
X-RAY DIFFRACTIONf_dihedral_angle_d13.7441609
X-RAY DIFFRACTIONf_chiral_restr0.077707
X-RAY DIFFRACTIONf_plane_restr0.004804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5991-1.6390.2711370.20785270X-RAY DIFFRACTION99
1.639-1.68340.25081490.21255374X-RAY DIFFRACTION100
1.6834-1.73290.23191420.20835355X-RAY DIFFRACTION100
1.7329-1.78880.24111430.19865390X-RAY DIFFRACTION100
1.7888-1.85270.24661440.2055369X-RAY DIFFRACTION100
1.8527-1.92690.23011490.19195377X-RAY DIFFRACTION100
1.9269-2.01460.22781450.19675377X-RAY DIFFRACTION100
2.0146-2.12080.24031460.19725367X-RAY DIFFRACTION100
2.1208-2.25370.21651430.19065392X-RAY DIFFRACTION100
2.2537-2.42760.21571440.19025379X-RAY DIFFRACTION100
2.4276-2.67190.21481490.19825393X-RAY DIFFRACTION100
2.6719-3.05830.22381420.19955407X-RAY DIFFRACTION100
3.0583-3.85240.20631420.19095265X-RAY DIFFRACTION97
3.8524-35.57110.21491330.18034916X-RAY DIFFRACTION90

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