+Open data
-Basic information
Entry | Database: PDB / ID: 4k4y | ||||||
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Title | Coxsackievirus B3 polymerase elongation complex (r2+1_form) | ||||||
Components |
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Keywords | Transferase/rna / polymerase / RNA-dependent RNA polymerase / protein-RNA complex / Transferase-rna complex | ||||||
Function / homology | Function and homology information 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 / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human coxsackievirus B3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Gong, P. / Peersen, O.B. | ||||||
Citation | Journal: Plos One / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k4y.cif.gz | 460.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k4y.ent.gz | 370.1 KB | Display | PDB format |
PDBx/mmJSON format | 4k4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k4y_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4k4y_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4k4y_validation.xml.gz | 77.4 KB | Display | |
Data in CIF | 4k4y_validation.cif.gz | 106.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/4k4y ftp://data.pdbj.org/pub/pdb/validation_reports/k4/4k4y | HTTPS FTP |
-Related structure data
Related structure data | 4k4sC 4k4tC 4k4uC 4k4vC 4k4wC 4k4xC 4k4zC 4k50C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
-RNA chain , 2 types, 8 molecules BFJNDHLP
#2: RNA chain | Mass: 7629.574 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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-Protein / DNA/RNA hybrid , 2 types, 8 molecules AEIMCGKO
#1: Protein | Mass: 53624.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coxsackievirus B3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66338, UniProt: Q5UEA2*PLUS #3: DNA/RNA hybrid | Mass: 4799.939 Da / Num. of mol.: 4 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 391 molecules
#5: Chemical | ChemComp-DCT / #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / 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: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.72→45.06 Å / Num. obs: 70840 / % possible obs: 97.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 1.92 % / Rmerge(I) obs: 0.097 / Χ2: 1.03 / Net I/σ(I): 5 / Scaling rejects: 1027 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→43.762 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7546 / SU ML: 0.37 / σ(F): 1.96 / Phase error: 30.71 / 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: 169.4 Å2 / Biso mean: 50.9641 Å2 / Biso min: 22.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→43.762 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: 25
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