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Yorodumi- PDB-1qa7: CRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ... -
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-Basic information
Entry | Database: PDB / ID: 1qa7 | ||||||
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Title | CRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ITS INHIBITOR AND IMPLICATIONS FOR THE POLYPROTEIN PROCESSING IN HAV | ||||||
Components | HAV 3C PROTEINASE | ||||||
Keywords | hydrolase/hydrolase inhibitor / CHYMOTRYPSIN-LIKE CYSTEINE PROTEINASE VIRAL PROTEASE P'-SITE INHIBITOR / HYDROLASE / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of toll-like receptor 3 signaling pathway / icosahedral viral capsid / host cell mitochondrial outer membrane / RNA-protein covalent cross-linking / : / : / virion assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C ...negative regulation of toll-like receptor 3 signaling pathway / icosahedral viral capsid / host cell mitochondrial outer membrane / RNA-protein covalent cross-linking / : / : / virion assembly / 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 / membrane => GO:0016020 / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bergmann, E.M. / Cherney, M.M. / Mckendrick, J. / Vederas, J.C. / James, M.N.G. | ||||||
Citation | Journal: Virology / Year: 1999 Title: Crystal structure of an inhibitor complex of the 3C proteinase from hepatitis A virus (HAV) and implications for the polyprotein processing in HAV. Authors: Bergmann, E.M. / Cherney, M.M. / Mckendrick, J. / Frormann, S. / Luo, C. / Malcolm, B.A. / Vederas, J.C. / James, M.N. #1: Journal: J.Virol. / Year: 1997 Title: The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition Authors: Bergmann, E.M. / Mosimann, S.C. / Chernaia, M.M. / Malcolm, B.A. / James, M.N.G. #2: Journal: Handbook of Proteolytic Enzymes / Year: 1998 Title: Hepatitis A virus picornain 3C Authors: Bergmann, E.M. #3: Journal: Handbook of Exp. Pharmacol., Vol. Proteases as Targets for Therapy Year: 1999 Title: The 3C proteinases of picornaviruses and other positive-sense, single-stranded RNA viruses Authors: Bergmann, E.M. / James, M.N.G. #4: Journal: Biochemistry / Year: 1992 Title: Expression and characterization of recombinant hepatitis A virus 3C proteinase Authors: Malcolm, B.A. / Chin, S.M. / Jewell, D.A. / Stratton-Thomas, J.R. / Thudium, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qa7.cif.gz | 189.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qa7.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qa7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/1qa7 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/1qa7 | HTTPS FTP |
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-Related structure data
Related structure data | 1havS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 23828.469 Da / Num. of mol.: 4 / Fragment: HAV 3C PROTEINASE / Mutation: C24S, F82A Source method: isolated from a genetically manipulated source Details: PROTEINASE CHEMICALLY BONDED TO INHIBITOR ACE-VAL-NFA. IT WAS CHEMICALLY SYNTHESIZED AS IODOACETYL-VALYL-PHENYLALANYL AMIDE Source: (gene. exp.) Hepatitis A virus / Genus: Hepatovirus / Plasmid: PHAV3-CEX / Production host: Escherichia coli (E. coli) / References: UniProt: P26582, UniProt: P08617*PLUS #2: Chemical | ChemComp-IVF / #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-GOL / | #5: 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: 2.17 Å3/Da / Density % sol: 43.29 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM TRIS, 5% DMSO, 18% PEG 8000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. all: 64826 / Num. obs: 59384 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.157 / Num. unique all: 4001 / % possible all: 74.7 |
Reflection | *PLUS Num. measured all: 494113 |
Reflection shell | *PLUS % possible obs: 74.7 % / Num. unique obs: 4001 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1hav Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: no non-crystallographic restraints
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 6.5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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