+Open data
-Basic information
Entry | Database: PDB / ID: 5jun | ||||||
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Title | PB2 bound to an azaindole inhibitor | ||||||
Components | Polymerase basic protein 2 | ||||||
Keywords | RNA BINDING PROTEIN / flu / polymerase / nucleotide binding / inhibitor | ||||||
Function / homology | Function and homology information cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.69 Å | ||||||
Authors | Jacobs, M.D. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Discovery of Novel, Orally Bioavailable beta-Amino Acid Azaindole Inhibitors of Influenza PB2. Authors: Farmer, L.J. / Clark, M.P. / Boyd, M.J. / Perola, E. / Jones, S.M. / Tsai, A. / Jacobs, M.D. / Bandarage, U.K. / Ledeboer, M.W. / Wang, T. / Deng, H. / Ledford, B. / Gu, W. / Duffy, J.P. / ...Authors: Farmer, L.J. / Clark, M.P. / Boyd, M.J. / Perola, E. / Jones, S.M. / Tsai, A. / Jacobs, M.D. / Bandarage, U.K. / Ledeboer, M.W. / Wang, T. / Deng, H. / Ledford, B. / Gu, W. / Duffy, J.P. / Bethiel, R.S. / Shannon, D. / Byrn, R.A. / Leeman, J.R. / Rijnbrand, R. / Bennett, H.B. / O'Brien, C. / Memmott, C. / Nti-Addae, K. / Bennani, Y.L. / Charifson, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jun.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jun.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/5jun ftp://data.pdbj.org/pub/pdb/validation_reports/ju/5jun | HTTPS FTP |
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-Related structure data
Related structure data | 5jurC 4nceS C: citing same article (ref.) S: Starting model for refinement |
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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: 19174.324 Da / Num. of mol.: 1 Fragment: Influenza RNA-dependent RNA polymerase subunit PB2 Source method: isolated from a genetically manipulated source Details: artifact / Source: (gene. exp.) Influenza A virus / Strain: A/Beijing/39/1975 H3N2 / Gene: PB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q30NP1 |
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#2: Chemical | ChemComp-6NU / ( |
#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: 2.73 Å3/Da / Density % sol: 54.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well ...Details: 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well solution (1.5 M sodium formate, 100 mM sodium citrate, pH 4.7, 10 mM dithiothreitol) suspended over 1 mL of well solution, crystals transferred to a soaking solution (3.25 M sodium formate, 100 mM sodium citrate, pH 4.7) containing 1 mM inhibitor, incubated approximately 15 hours at room temperature, and then transferred to a cryo-preservative solution (soaking solution with 25% v/v glycerol) prior to freezing in liquid nitrogen |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 19, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.598→29.64 Å / Num. obs: 6190 / % possible obs: 95.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 69.46 Å2 / Rsym value: 0.052 / Net I/av σ(I): 14.2 / Net I/σ(I): 23.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4NCE Resolution: 2.69→29.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.824 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.249
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Displacement parameters | Biso max: 180.75 Å2 / Biso mean: 64.59 Å2 / Biso min: 23.69 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.69→29.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→3.01 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: -37.9523 Å / Origin y: -0.3006 Å / Origin z: 2.7032 Å
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Refinement TLS group | Selection details: { A|* } |