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Open data
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Basic information
Entry | Database: PDB / ID: 4y3c | ||||||
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Title | I304V 3D polymerase mutant of EMCV | ||||||
![]() | 3D polymerase | ||||||
![]() | VIRAL PROTEIN / RNA dependent RNA polymerase Cardiovirus Inhibitor resistance | ||||||
Function / homology | ![]() positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity ...positive stranded viral RNA replication / host cell nucleolus / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Verdaguer, N. / Ferrer-Orta, C. / Vives-Adrian, L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 915.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.5 KB | Display | ![]() |
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Full document | ![]() | 479.8 KB | Display | |
Data in XML | ![]() | 87.4 KB | Display | |
Data in CIF | ![]() | 117.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y2aC ![]() 4y2cC ![]() 4y34C ![]() 4nz0S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
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Unit cell |
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Components
#1: Protein | Mass: 52230.477 Da / Num. of mol.: 6 / Mutation: I304V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P12296, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 4.0M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.45 Å / Num. obs: 73423 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NZ0 Resolution: 3.2→138.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU B: 64.307 / SU ML: 0.466 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / 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: 96.599 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→138.96 Å
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