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Yorodumi- PDB-4zi0: Endonuclease inhibitor bound to influenza strain H1N1 polymerase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zi0 | ||||||
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Title | Endonuclease inhibitor bound to influenza strain H1N1 polymerase acidic subunit N-terminal region without a chelation to the metal ions in the active site | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis ...cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / vRNP Assembly / Viral Messenger RNA Synthesis / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Viral mRNA Translation / cap snatching / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Model details | RNA binding protein | ||||||
Authors | Fudo, S. / Yamamoto, N. / Nukaga, M. / Odagiri, T. / Tashiro, M. / Neya, S. / Hoshino, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit Authors: Fudo, S. / Yamamoto, N. / Nukaga, M. / Odagiri, T. / Tashiro, M. / Hoshino, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zi0.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zi0.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zi0_validation.pdf.gz | 684.4 KB | Display | wwPDB validaton report |
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Full document | 4zi0_full_validation.pdf.gz | 684.7 KB | Display | |
Data in XML | 4zi0_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4zi0_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/4zi0 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/4zi0 | HTTPS FTP |
-Related structure data
Related structure data | 4zhzC 4zqqC 5fddC 5fdgC 5i13C 4m5qS 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: 22300.494 Da / Num. of mol.: 1 / Fragment: endonuclease, residues 1-50, 73-196 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) Strain: A/Puerto Rico/8/1934 H1N1 / Gene: PA / Plasmid: pET50b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P03433 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-4P9 / | #5: 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: 3.17 Å3/Da / Density % sol: 61.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 100 mM MES, 1.1 M ammonium sulfate, 0.1 M potassium chloride, 9 % trehalose |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 27032 / % possible obs: 98.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 37.59 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Χ2: 1.031 / Net I/av σ(I): 36.194 / Net I/σ(I): 16.8 / Num. measured all: 374092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 4M5Q Resolution: 1.802→32.278 Å / FOM work R set: 0.8247 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.77 / 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: 106.38 Å2 / Biso mean: 44.67 Å2 / Biso min: 24.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.802→32.278 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: 10
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