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Yorodumi- PDB-2cxv: Dual Modes of Modification of Hepatitis A Virus 3C Protease by a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cxv | ||||||
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Title | Dual Modes of Modification of Hepatitis A Virus 3C Protease by a Serine-Derived betaLactone: Selective Crystallization and High-resolution Structure of the His-102 Adduct | ||||||
Components | Probable protein P3C | ||||||
Keywords | HYDROLASE / Hepatitis A / picornavirus / 3C / cysteine protease / inhibitor / beta-Lactone | ||||||
Function / homology | Function and homology information host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Human hepatitis A virus Hu/Northern Africa/MBB/1978 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Yin, J. / Bergmann, E.M. / Cherney, M.M. / Lall, M.S. / Jain, R.P. / Vederas, J.C. / James, M.N.G. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2005 Title: Dual Modes of Modification of Hepatitis A Virus 3C Protease by a Serine-derived beta-Lactone: Selective Crystallization and Formation of a Functional Catalytic Triad in the Active Site Authors: Yin, J. / Bergmann, E.M. / Cherney, M.M. / Lall, M.S. / Jain, R.P. / Vederas, J.C. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cxv.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cxv.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cxv_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 2cxv_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 2cxv_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 2cxv_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/2cxv ftp://data.pdbj.org/pub/pdb/validation_reports/cx/2cxv | HTTPS FTP |
-Related structure data
Related structure data | 2a4oC 1havS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | the biological assembly of this protein is likely to be a monomer. |
-Components
#1: Protein | Mass: 24119.771 Da / Num. of mol.: 1 / Mutation: C24S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human hepatitis A virus Hu/Northern Africa/MBB/1978 Genus: Hepatovirus / Species: Hepatitis A virus / Strain: MBB / Gene: 3C / Plasmid: pHAV-3CEX / Production host: Escherichia coli (E. coli) / Strain (production host): D1210 / References: UniProt: P13901, picornain 3C |
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#2: Chemical | ChemComp-BBL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40.2 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, Tris-HCl, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.8857 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2000 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8857 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 40672 / Num. obs: 39711 / % possible obs: 97.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Rmerge(I) obs: 0.037 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.4→1.44 Å / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 5.8 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HAV Resolution: 1.4→18.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.004 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.569 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.381 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→18.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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