+Open data
-Basic information
Entry | Database: PDB / ID: 5f8g | ||||||
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Title | Enterovirus 71 Polymerase Elongation Complex (C1S1 Form) | ||||||
Components |
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Keywords | TRANSFERASE/RNA / polymerase-RNA complex / elongation / nucleotide addition cycle / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / 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 / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterovirus A71 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||
Authors | Shu, B. / Gong, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation Authors: Shu, B. / Gong, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f8g.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f8g.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 5f8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/5f8g ftp://data.pdbj.org/pub/pdb/validation_reports/f8/5f8g | HTTPS FTP |
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-Related structure data
Related structure data | 5f8hC 5f8iC 5f8jC 5f8lC 5f8mC 5f8nC 3ol6S 5f8o 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: 53380.406 Da / Num. of mol.: 1 / Fragment: UNP residues 1732-2193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: E5RPG3 |
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#2: RNA chain | Mass: 11260.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: RNA chain | Mass: 5201.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-ZN / |
#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: 2.68 Å3/Da / Density % sol: 54.16 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.085 M MES pH 6.5, 25.5 % (w/v) PEG 5000 monomethyl ether, 15 %(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.78→60 Å / Num. obs: 19258 / % possible obs: 97.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 43.71 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.054 / Rrim(I) all: 0.129 / Χ2: 0.944 / Net I/av σ(I): 13.625 / Net I/σ(I): 6.8 / Num. measured all: 104922 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OL6 Resolution: 2.78→48.774 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.45 / 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: 110.31 Å2 / Biso mean: 43.6799 Å2 / Biso min: 18.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.78→48.774 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: 7
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