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Yorodumi- PDB-5bpv: Crystal Structure of Zaire ebolavirus VP35 RNA binding domain mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bpv | ||||||
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Title | Crystal Structure of Zaire ebolavirus VP35 RNA binding domain mutant I278A | ||||||
Components | Polymerase cofactor VP35 | ||||||
Keywords | VIRAL PROTEIN / Polymerase cofactor / Interferon inhibitor | ||||||
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 / virion component / 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 / MOLECULAR REPLACEMENT / Resolution: 1.952 Å | ||||||
Authors | Fadda, V. / Cannas, V. / Zinzula, L. / Distinto, S. / Daino, G.L. / Bianco, G. / Corona, A. / Esposito, F. / Alcaro, S. / Maccioni, E. ...Fadda, V. / Cannas, V. / Zinzula, L. / Distinto, S. / Daino, G.L. / Bianco, G. / Corona, A. / Esposito, F. / Alcaro, S. / Maccioni, E. / Tramontano, E. / Taylor, G.L. | ||||||
Citation | Journal: to be published Title: Crystal Structure of Zaire ebolavirus VP35 RNA binding domain mutant I278A Authors: Fadda, V. / Cannas, V. / Zinzula, L. / Distinto, S. / Daino, G.L. / Bianco, G. / Corona, A. / Esposito, F. / Alcaro, S. / Maccioni, E. / Tramontano, E. / Taylor, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bpv.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bpv.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 5bpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/5bpv ftp://data.pdbj.org/pub/pdb/validation_reports/bp/5bpv | HTTPS FTP |
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-Related structure data
Related structure data | 3fkeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13655.817 Da / Num. of mol.: 2 / Fragment: RNA binding domain, UNP residues 217-340 / Mutation: I278A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zaire ebolavirus / Gene: VP35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V1Q9, UniProt: Q05127*PLUS #2: 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: 2.24 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium sodium tartrate tetrahydrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 3, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.952→48.522 Å / Num. all: 18397 / Num. obs: 18397 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.23 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Rsym value: 0.104 / Net I/av σ(I): 5.72 / Net I/σ(I): 11.8 / Num. measured all: 122680 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FKE Resolution: 1.952→13.905 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.82 / 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: 99.39 Å2 / Biso mean: 22.7715 Å2 / Biso min: 6.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.952→13.905 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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