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Open data
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Basic information
Entry | Database: PDB / ID: 4k4x | ||||||
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Title | Coxsackievirus B3 polymerase elongation complex (r2_form), rna | ||||||
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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 / 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 ...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 / 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 / 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 / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / 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 | ![]() | 455.7 KB | Display | ![]() |
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PDB format | ![]() | 366.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4k4sC ![]() 4k4tC ![]() 4k4uC ![]() 4k4vC ![]() 4k4wC ![]() 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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3 | ![]()
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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: 53624.203 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1724-2185 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q66338, UniProt: Q5UEA2*PLUS, RNA-directed RNA polymerase |
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-RNA chain , 3 types, 12 molecules BFJNCGKODHLP
#2: RNA chain | Mass: 7629.574 Da / Num. of mol.: 4 / Source method: obtained synthetically #3: RNA chain | Mass: 4526.756 Da / Num. of mol.: 4 / Source method: obtained synthetically #4: RNA chain | Mass: 2974.854 Da / Num. of mol.: 4 / Source method: obtained synthetically |
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-Non-polymers , 3 types, 737 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-MG / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.44 % |
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Crystal grow | Temperature: 289 K / pH: 8.5 Details: 0.17 M sodium acetate, 0.085 M Tris, 25.5% PEG 4000, and 15% glycerol and directly frozen, pH 8.5, 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: 2.37→48.78 Å / Num. obs: 109647 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 1.99 % / Biso Wilson estimate: 41.68 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.37→2.45 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 1.5 / % possible all: 96.6 |
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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 mean: 47.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→44.01 Å
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Refine LS restraints |
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LS refinement shell |
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