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Yorodumi- PDB-5zit: Crystal structure of human Enterovirus D68 RdRp in complex with NADPH -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zit | |||||||||
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Title | Crystal structure of human Enterovirus D68 RdRp in complex with NADPH | |||||||||
Components | RdRpRNA-dependent RNA polymerase | |||||||||
Keywords | RNA BINDING PROTEIN / EVD68-RdRp / Complex / Inhibitor / NADPH-Na4 / Structure-based design | |||||||||
Function / homology | Function and homology information : / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...: / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Enterovirus D68 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.196 Å | |||||||||
Authors | Wang, M.L. / Li, L. / Chen, Y.P. / Jiang, H. / Zhang, Y. / Su, D. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Structure of the enterovirus D68 RNA-dependent RNA polymerase in complex with NADPH implicates an inhibitor binding site in the RNA template tunnel. Authors: Li, L. / Wang, M. / Chen, Y. / Hu, T. / Yang, Y. / Zhang, Y. / Bi, G. / Wang, W. / Liu, E. / Han, J. / Lu, T. / Su, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zit.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zit.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/5zit ftp://data.pdbj.org/pub/pdb/validation_reports/zi/5zit | HTTPS FTP |
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-Related structure data
Related structure data | 6l4rC 5xe0S 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: 51913.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus D68 / Production host: Escherichia coli (E. coli) References: UniProt: I6TFG7, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.52 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris, PH 8.0, 3.5M NH4Cl, 10mM Chromic chroride hexahydrate,5mM NADPH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97775 Å / Relative weight: 1 |
Reflection | Resolution: 3.19→50 Å / Num. obs: 12153 / % possible obs: 100 % / Redundancy: 23.8 % / Rmerge(I) obs: 0.281 / Net I/σ(I): 12.67 |
Reflection shell | Resolution: 3.19→3.28 Å / Redundancy: 25.9 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 6 / Num. unique obs: 948 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XE0 Resolution: 3.196→46.428 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36.09 / 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: 168.86 Å2 / Biso mean: 64.6655 Å2 / Biso min: 20.87 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.196→46.428 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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