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Yorodumi- PDB-4ijf: Crystal structure of the Zaire ebolavirus VP35 interferon inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ijf | ||||||
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Title | Crystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain K222A/R225A/K248A/K251A mutant | ||||||
Components | Polymerase cofactor VP35 | ||||||
Keywords | VIRAL PROTEIN / IFN inhibition / polymerase cofactor / RNA binding protein / interferon antagonism / dsRNA / virus | ||||||
Function / homology | Function and homology information suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / molecular sequestering activity ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / molecular sequestering activity / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / negative regulation of gene expression / RNA binding Similarity search - Function | ||||||
Biological species | Zaire ebolavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å | ||||||
Authors | Binning, J.B. / Wang, T. / Leung, D.W. / Xu, W. / Borek, D. / Amarasinghe, G.K. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Development of RNA Aptamers Targeting Ebola Virus VP35. Authors: Binning, J.M. / Wang, T. / Luthra, P. / Shabman, R.S. / Borek, D.M. / Liu, G. / Xu, W. / Leung, D.W. / Basler, C.F. / Amarasinghe, G.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ijf.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ijf.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 4ijf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ijf_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 4ijf_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | 4ijf_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 4ijf_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/4ijf ftp://data.pdbj.org/pub/pdb/validation_reports/ij/4ijf | HTTPS FTP |
-Related structure data
Related structure data | 4ijeC 3fkeS 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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-Components
#1: Protein | Mass: 13852.986 Da / Num. of mol.: 1 Fragment: interferon inhibitory domain (UNP residues 218-340) Mutation: K222A, R225A, K248A, K251A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: VP35 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127 |
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#2: 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: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, 30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793378 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793378 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 5063 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.074 / Χ2: 0.868 / Net I/σ(I): 12.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FKE Resolution: 2.506→41.104 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7685 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.99 Å2 / Biso mean: 50.2847 Å2 / Biso min: 16.93 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.506→41.104 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.506→41.1091 Å / Total num. of bins used: 1
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Refinement TLS params. | Method: refined / Origin x: 26.6011 Å / Origin y: -24.9494 Å / Origin z: 15.0614 Å
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Refinement TLS group |
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