+Open data
-Basic information
Entry | Database: PDB / ID: 4ibb | ||||||
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Title | Ebola virus VP35 bound to small molecule | ||||||
Components | Polymerase cofactor VP35 | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION inhibitor / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Interferon inhibitory domain / TRANSCRIPTION-TRANSCRIPTION inhibitor complex | ||||||
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 | Ebola virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å | ||||||
Authors | Brown, C.S. / Leung, D.W. / Xu, W. / Borek, D.M. / Otwinowski, Z. / Ramanan, P. / Stubbs, A.J. / Peterson, D.S. / Binning, J.M. / Amarasinghe, G.K. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity. Authors: Brown, C.S. / Lee, M.S. / Leung, D.W. / Wang, T. / Xu, W. / Luthra, P. / Anantpadma, M. / Shabman, R.S. / Melito, L.M. / Macmillan, K.S. / Borek, D.M. / Otwinowski, Z. / Ramanan, P. / ...Authors: Brown, C.S. / Lee, M.S. / Leung, D.W. / Wang, T. / Xu, W. / Luthra, P. / Anantpadma, M. / Shabman, R.S. / Melito, L.M. / Macmillan, K.S. / Borek, D.M. / Otwinowski, Z. / Ramanan, P. / Stubbs, A.J. / Peterson, D.S. / Binning, J.M. / Tonelli, M. / Olson, M.A. / Davey, R.A. / Ready, J.M. / 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 | 4ibb.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ibb.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ibb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ibb_validation.pdf.gz | 996.7 KB | Display | wwPDB validaton report |
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Full document | 4ibb_full_validation.pdf.gz | 1000.5 KB | Display | |
Data in XML | 4ibb_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4ibb_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibb ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibb | HTTPS FTP |
-Related structure data
Related structure data | 4ibcC 4ibdC 4ibeC 4ibfC 4ibgC 4ibiC 4ibjC 4ibkC 4ibh 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14210.523 Da / Num. of mol.: 2 / Fragment: unp residues 215-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus / Strain: Mayinga-76 / Gene: VP35 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127 #2: Chemical | #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: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM magnesium acetate, pH7.5, 15% PEG3350, 10% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9785724 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785724 Å / Relative weight: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.752→36.111 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.19 / σ(F): 1.37 / Phase error: 28.49 / 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 mean: 24.0601 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.752→36.111 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.097 Å / Origin y: 29.2881 Å / Origin z: 11.713 Å
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Refinement TLS group |
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