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Yorodumi- PDB-8c1n: FMDV 3D polymerase in complex with 3B1 protein solved in P212121 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c1n | ||||||
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Title | FMDV 3D polymerase in complex with 3B1 protein solved in P212121 space group | ||||||
Components |
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Keywords | VIRAL PROTEIN / RNA dependent RNA polymerase FMDV Picornavirus 3B VPg | ||||||
Function / homology | Function and homology information L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization ...L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / 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 / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Foot-and-mouth disease virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ferrer-Orta, C. / Veraguer, N. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Plos Pathog. / Year: 2023 Title: Dual role of the foot-and-mouth disease virus 3B1 protein in the replication complex: As protein primer and as an essential component to recruit 3Dpol to membranes. Authors: Ferrer-Orta, C. / Ferrero, D.S. / Verdaguer, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c1n.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c1n.ent.gz | 168 KB | Display | PDB format |
PDBx/mmJSON format | 8c1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/8c1n ftp://data.pdbj.org/pub/pdb/validation_reports/c1/8c1n | HTTPS FTP |
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-Related structure data
Related structure data | 8c2pC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 54126.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: P03311, RNA-directed RNA polymerase #2: Protein/peptide | | Mass: 2666.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus / References: UniProt: P03311 |
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-Non-polymers , 4 types, 613 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.43 Å3/Da / Density % sol: 49.43 % Description: Dimer of 3D polymerases with a 3B1 protein connecting them |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M Ammonium acetate 25% PEG 4K 0.1M HEPES pH 6.5 4% gamma-butyrolactone. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.234 Å / Num. obs: 113370 / % possible obs: 97.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.33 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 14640 / Rpim(I) all: 0.608 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.75 Å / SU ML: 0.2151 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1367 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 20.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→44.75 Å
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Refine LS restraints |
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LS refinement shell |
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