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- PDB-5i13: Endonuclease inhibitor 2 bound to influenza strain H1N1 polymeras... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i13 | |||||||||
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Title | Endonuclease inhibitor 2 bound to influenza strain H1N1 polymerase acidic subunit N-terminal region at pH 7.0 | |||||||||
![]() | Polymerase acidic protein | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Hydrolase-Hydrolase Inhibitor complex | |||||||||
Function / homology | ![]() 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 / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Viral mRNA Translation / 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
Model details | RNA binding protein | |||||||||
![]() | Fudo, S. / Yamamoto, N. / Nukaga, M. / Odagiri, T. / Tashiro, M. / Hoshino, T. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.9 KB | Display | ![]() |
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PDB format | ![]() | 38 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 961 KB | Display | ![]() |
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Full document | ![]() | 961.8 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zhzC ![]() 4zi0C ![]() 4zqqSC ![]() 5fddC ![]() 5fdgC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: A/Puerto Rico/8/1934 H1N1 / Gene: PA / Plasmid: pET50b(+) / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Crystals were grown with the reservoir containing 100 mM MES, 1.1 M ammonium sulfate, 0.1 M potassium chloride and 9 % trehalose at pH 5.8. Crystal was then soaked with the ligand solution at pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 16066 / % possible obs: 98 % / Redundancy: 9 % / Rmerge(I) obs: 0.074 / Net I/av σ(I): 25.351 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 9 % / Rmerge(I) obs: 1.034 / % possible all: 99.4 |
-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZQQ Resolution: 2.151→37.956 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.18 Å2 / Biso mean: 44.33 Å2 / Biso min: 20.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.151→37.956 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: 6
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