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Yorodumi- PDB-2ec0: RNA-dependent RNA polymerase of foot-and-mouth disease virus in c... -
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-Basic information
Entry | Database: PDB / ID: 2ec0 | ||||||
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Title | RNA-dependent RNA polymerase of foot-and-mouth disease virus in complex with a template-primer RNA and ATP | ||||||
Components |
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Keywords | TRANSFERASE/RNA / RNA-dependent RNA polymerase / 3D polymerase / polymerase / foot-and- mouth disease virus / TRANSFERASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Foot-and-mouth disease virus C-S8c1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Sequential structures provide insights into the fidelity of RNA replication Authors: Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N. #1: Journal: Embo J. / Year: 2006 Title: The structure of a protein primer-polymerase complex in the initiation of genome replication Authors: Ferrer-Orta, C. / Arias, A. / Agudo, R. / Perez-Luque, R. / Escarmis, R. / Domingo, E. / Verdaguer, N. #2: Journal: Curr.Opin.Struct.Biol. / Year: 2006 Title: A comparison of viral RNA-dependent RNA polymerases Authors: Ferrer-Orta, C. / Arias, A. / Escarmis, C. / Verdaguer, N. #3: Journal: J.Biol.Chem. / Year: 2004 Title: Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA Authors: Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N. #4: Journal: J.Mol.Biol. / Year: 2005 Title: Mutant viral polymerase in the transition of virus to error catastrophe identifies a critical site for RNA binding Authors: Arias, A. / Agudo, R. / Ferrer-Orta, C. / Perez-Luque, R. / Airaksinen, A. / Brocchi, E. / Domingo, E. / Verdaguer, N. / Escarmis, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ec0.cif.gz | 215.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ec0.ent.gz | 169.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ec0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/2ec0 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/2ec0 | HTTPS FTP |
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-Related structure data
Related structure data | 2e9rC 2e9tC 2e9zC 1u09S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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-Components
-RNA chain , 2 types, 4 molecules BECF
#1: RNA chain | Mass: 2541.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA template #2: RNA chain | Mass: 2235.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA primer |
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-Protein , 1 types, 2 molecules AD
#3: Protein | Mass: 53486.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus C-S8c1 / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: C-S8C1 / Gene: 3D / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q0QEE1, UniProt: Q9QCE4*PLUS, RNA-directed RNA polymerase |
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-Non-polymers , 3 types, 118 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.28 Å3/Da / Density % sol: 46.11 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG 4000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 197 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2004 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 30133 / Num. obs: 28495 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.075 / Rsym value: 0.054 / Net I/σ(I): 7.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U09 Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 39.37 / SU ML: 0.384 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.519 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.027 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.75→2.82 Å / Total num. of bins used: 20
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