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Yorodumi- PDB-4ncm: Influenza polymerase basic protein 2 (PB2) bound to a small-molec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ncm | ||||||
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Title | Influenza polymerase basic protein 2 (PB2) bound to a small-molecule inhibitor | ||||||
Components | Polymerase basic protein 2 | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION INHIBITOR / RNA-dependent RNA polymerase / transcription / PB2 subunit / influenza virus / cap-binding domain / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex | ||||||
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 / virus-mediated perturbation of host defense response / DNA-templated transcription ...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 / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.82 Å | ||||||
Authors | Jacobs, M.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Discovery of a Novel, First-in-Class, Orally Bioavailable Azaindole Inhibitor (VX-787) of Influenza PB2. Authors: Clark, M.P. / Ledeboer, M.W. / Davies, I. / Byrn, R.A. / Jones, S.M. / Perola, E. / Tsai, A. / Jacobs, M. / Nti-Addae, K. / Bandarage, U.K. / Boyd, M.J. / Bethiel, R.S. / Court, J.J. / Deng, ...Authors: Clark, M.P. / Ledeboer, M.W. / Davies, I. / Byrn, R.A. / Jones, S.M. / Perola, E. / Tsai, A. / Jacobs, M. / Nti-Addae, K. / Bandarage, U.K. / Boyd, M.J. / Bethiel, R.S. / Court, J.J. / Deng, H. / Duffy, J.P. / Dorsch, W.A. / Farmer, L.J. / Gao, H. / Gu, W. / Jackson, K. / Jacobs, D.H. / Kennedy, J.M. / Ledford, B. / Liang, J. / Maltais, F. / Murcko, M. / Wang, T. / Wannamaker, M.W. / Bennett, H.B. / Leeman, J.R. / McNeil, C. / Taylor, W.P. / Memmott, C. / Jiang, M. / Rijnbrand, R. / Bral, C. / Germann, U. / Nezami, A. / Zhang, Y. / Salituro, F.G. / 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 | 4ncm.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ncm.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ncm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ncm_validation.pdf.gz | 804.9 KB | Display | wwPDB validaton report |
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Full document | 4ncm_full_validation.pdf.gz | 805.2 KB | Display | |
Data in XML | 4ncm_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 4ncm_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/4ncm ftp://data.pdbj.org/pub/pdb/validation_reports/nc/4ncm | HTTPS FTP |
-Related structure data
Related structure data | 4nceSC 4p1uC 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: 19174.324 Da / Num. of mol.: 1 / Fragment: CAP-BINDING DOMAIN / Mutation: R389K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/3/1975 H3N2 / Gene: PB2, polymerase basic protein 2 PB2 / Plasmid: pET28b.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P31345 |
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#2: Chemical | ChemComp-704 / |
#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: 2.76 Å3/Da / Density % sol: 55.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 0.7 uL of protein solution (9.7 mg/mL protein, 50 mM Tris buffer pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 5 mM m7GTP) was mixed with 0.35 uL Hampton Research Silver Bullet ...Details: 0.7 uL of protein solution (9.7 mg/mL protein, 50 mM Tris buffer pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 5 mM m7GTP) was mixed with 0.35 uL Hampton Research Silver Bullet screening reagent #36. This mixture was combined with 0.35 uL of well solution (approximately 1.3 M sodium formate, 100 mM sodium citrate buffer pH 4.6, 5 mM dithiothreitol) and suspended over 1 mL of well solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.818→43.186 Å / Num. all: 5135 / Num. obs: 4894 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 69.16 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 4NCE Resolution: 2.82→41.05 Å / Cor.coef. Fo:Fc: 0.9393 / Cor.coef. Fo:Fc free: 0.9319 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 54.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.277 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→41.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→3.15 Å / Total num. of bins used: 5
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