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Yorodumi- PDB-5zqg: Complex structure of PEDV 3CLpro mutant (C144A) with NEMO-231 pep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zqg | ||||||
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Title | Complex structure of PEDV 3CLpro mutant (C144A) with NEMO-231 peptite substrate | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / 3C-like protease / complex structure / NEMO / PEDV 3CLpro / mutant / C144A / HYDROLASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / viral genome replication / 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity ...host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / viral genome replication / 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease 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 / 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 | ||||||
Biological species | Porcine epidemic diarrhea virus Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Gang, Y. / Chen, J.Y. / Dang, W. / Xiao, S.B. / Peng, G.Q. | ||||||
Citation | Journal: To Be Published Title: Complex structure of PEDV 3CLpro mutant (C144A) with NEMO peptite substrate Authors: Gang, Y. / Chen, J.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zqg.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zqg.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/5zqg ftp://data.pdbj.org/pub/pdb/validation_reports/zq/5zqg | HTTPS FTP |
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-Related structure data
Related structure data | 4xfqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | | Mass: 1300.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.6→1.66 Å / Rpim(I) all: 0.084 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XFQ Resolution: 1.6→35.562 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→35.562 Å
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Refine LS restraints |
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LS refinement shell |
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