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Open data
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Basic information
Entry | Database: PDB / ID: 4k50 | ||||||
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Title | Rhinovirus 16 polymerase elongation complex (r1_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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / 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 ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / 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 / symbiont-mediated suppression of host gene expression / DNA replication / 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 | ![]() | 480.1 KB | Display | ![]() |
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PDB format | ![]() | 385.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 544.8 KB | Display | ![]() |
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Full document | ![]() | 573.8 KB | Display | |
Data in XML | ![]() | 73.5 KB | Display | |
Data in CIF | ![]() | 103.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k4sC ![]() 4k4tC ![]() 4k4uC ![]() 4k4vC ![]() 4k4wC ![]() 4k4xC ![]() 4k4yC ![]() 4k4zC 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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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules AEIM
#1: Protein | Mass: 52344.035 Da / Num. of mol.: 4 / Fragment: unp residues 1694-2153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-RNA chain , 2 types, 8 molecules BFJNCGKO
#2: RNA chain | Mass: 11283.772 Da / Num. of mol.: 4 / Source method: obtained synthetically #3: RNA chain | Mass: 4563.828 Da / Num. of mol.: 4 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 434 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.16 M ammonium sulfate, 0.08 M sodium acetate, pH 4.6, 20% (w/v) PEG 4000, and 20% (v/v) glycerol and directly frozen , VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-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: 2.93→49.07 Å / Num. obs: 61473 / % possible obs: 98.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 1.98 % / Rmerge(I) obs: 0.108 / Χ2: 1.02 / Net I/σ(I): 5.1 / Scaling rejects: 919 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 162.75 Å2 / Biso mean: 37.7811 Å2 / Biso min: 9.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.93→45.303 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: 22
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