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Open data
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Basic information
Entry | Database: PDB / ID: 4k4u | ||||||
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Title | Poliovirus polymerase elongation complex (r5_form) | ||||||
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![]() | Transferase/rna / polymerase / RNA-dependent RNA polymerase / protein-RNA complex / Transferase-rna complex | ||||||
Function / homology | ![]() symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / 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 / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gong, P. / Peersen, O.B. | ||||||
![]() | ![]() Title: Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts. Authors: Gong, P. / Kortus, M.G. / Nix, J.C. / Davis, R.E. / Peersen, O.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235 KB | Display | ![]() |
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PDB format | ![]() | 184.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 512.3 KB | Display | ![]() |
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Full document | ![]() | 532.2 KB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 51.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k4sC ![]() 4k4tC ![]() 4k4vC ![]() 4k4wC ![]() 4k4xC ![]() 4k4yC ![]() 4k4zC ![]() 4k50C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AE
#1: Protein | Mass: 53789.250 Da / Num. of mol.: 2 / Fragment: unp residues 1749-2209 / Mutation: L446D, C290M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-RNA chain , 3 types, 6 molecules BFCGHD
#2: RNA chain | Mass: 8240.921 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: RNA chain | Mass: 5201.168 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: RNA chain | Mass: 3665.266 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 2 types, 61 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 4.8%(v/v) isopropanol, 0.096 M tacsimate (Hampton Research), pH 8.5-9.0, 1.92-1.95 M ammonium sulfate, and 10-11%(v/v) glycerol and then gradually exchanged into a cryo stabilizer solution ...Details: 4.8%(v/v) isopropanol, 0.096 M tacsimate (Hampton Research), pH 8.5-9.0, 1.92-1.95 M ammonium sulfate, and 10-11%(v/v) glycerol and then gradually exchanged into a cryo stabilizer solution containing 4.8%(v/v) isopropanol, 0.096 M tacsimate, 1.95 M ammonium sulfate and 19-27%(v/v) xylitol prior to freezing, VAPOR DIFFUSION, SITTING DROP, temperature 289K PH range: 8.5-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→45.69 Å / Num. obs: 34198 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 2.01 % / Rmerge(I) obs: 0.047 / Χ2: 1.17 / Net I/σ(I): 9 / Scaling rejects: 520 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: 223.58 Å2 / Biso mean: 96.6887 Å2 / Biso min: 57.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→43.263 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: 12
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