+Open data
-Basic information
Entry | Database: PDB / ID: 4wfx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Coxsackievirus B3 Polymerase - F232L Mutant - NaCl Crystal Form | |||||||||
Components | RNA-directed RNA polymeraseRNA-dependent RNA polymerase | |||||||||
Keywords | TRANSFERASE / RNA-dependent RNA polymerase | |||||||||
Function / homology | Function and homology information : / symbiont-mediated perturbation of host gene expression / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 ...: / symbiont-mediated perturbation of host gene expression / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / 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 / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Coxsackievirus B3 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.808 Å | |||||||||
Authors | Peersen, O.B. / McDonald, S.M. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: J.Virol. / Year: 2015 Title: Structure-Function Relationships Underlying the Replication Fidelity of Viral RNA-Dependent RNA Polymerases. Authors: Campagnola, G. / McDonald, S. / Beaucourt, S. / Vignuzzi, M. / Peersen, O.B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wfx.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wfx.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 4wfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/4wfx ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wfx | HTTPS FTP |
---|
-Related structure data
Related structure data | 4wfyC 4wfzC 3ddkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 52443.031 Da / Num. of mol.: 1 / Fragment: unp residues 1724-2185 / Mutation: F232L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus B3 / Strain: Nancy / Plasmid: pET26/Ub / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03313, RNA-directed RNA polymerase | ||
---|---|---|---|
#2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.6 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7.5 / Details: 0.085 M HEPES, 3.655 M NaCl, 15% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: IMAGE PLATE / Date: Jun 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→52.6 Å / Num. obs: 74782 / % possible obs: 99.4 % / Redundancy: 12.5 % / Biso Wilson estimate: 23.49 Å2 / Net I/σ(I): 18.97 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ddk Resolution: 1.808→52.58 Å / FOM work R set: 0.8674 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.58 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.26 Å2 / Biso mean: 23.12 Å2 / Biso min: 3.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.808→52.58 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|