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Yorodumi- PDB-4y2a: Crystal Structure of Coxsackie Virus B3 3D polymerase in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y2a | ||||||
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Title | Crystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor | ||||||
Components | 3D polymerase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Polymerase / Picornavirus / Coxsackievirus / GPC-N114 / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 ...: / 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 / 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 / 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: 2.9 Å | ||||||
Authors | Vives-Adrian, L. / Ferrer-Orta, C. / Verdaguer, N. | ||||||
Citation | Journal: Plos Pathog. / Year: 2015 Title: The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family. Authors: van der Linden, L. / Vives-Adrian, L. / Selisko, B. / Ferrer-Orta, C. / Liu, X. / Lanke, K. / Ulferts, R. / De Palma, A.M. / Tanchis, F. / Goris, N. / Lefebvre, D. / De Clercq, K. / Leyssen, ...Authors: van der Linden, L. / Vives-Adrian, L. / Selisko, B. / Ferrer-Orta, C. / Liu, X. / Lanke, K. / Ulferts, R. / De Palma, A.M. / Tanchis, F. / Goris, N. / Lefebvre, D. / De Clercq, K. / Leyssen, P. / Lacroix, C. / Purstinger, G. / Coutard, B. / Canard, B. / Boehr, D.D. / Arnold, J.J. / Cameron, C.E. / Verdaguer, N. / Neyts, J. / van Kuppeveld, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y2a.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y2a.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 4y2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/4y2a ftp://data.pdbj.org/pub/pdb/validation_reports/y2/4y2a | HTTPS FTP |
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-Related structure data
Related structure data | 4y2cC 4y34C 4y3cC 3ddkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53001.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus B3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03313 | ||||
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#2: Chemical | ChemComp-1FS / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50 mM Tris pH 7.5, 24.5% (w/v) glycerol, 1.29 M ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→72.4 Å / Num. obs: 18099 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.081 / Rsym value: 0.08 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.9→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.415 / Rsym value: 0.357 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DDK Resolution: 2.9→72.36 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.271 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.695 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.837 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→72.36 Å
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