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Yorodumi- EMDB-2270: Average reconstruction of cryoEM poliovirus polymerase tubes with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2270 | |||||||||
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Title | Average reconstruction of cryoEM poliovirus polymerase tubes with (-32,6) helical symmetry | |||||||||
Map data | Helical reconstruction of wild-type poliovirus polymerase tubes n,l (1,0): -32, 5 n,l (0,1): 6, 30 Map has 2-fold symmetry around the helical axis. t= 170, u= 495 (l = 170n + 495m) dphi = 123.636364, dz = 6.071919 | |||||||||
Sample |
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Keywords | poliovirus polymerase / virus replication / helical reconstruction / cryoEM | |||||||||
Biological species | Human poliovirus 1 Mahoney | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 16.0 Å | |||||||||
Authors | Wang J / Bullitt E | |||||||||
Citation | Journal: J Mol Biol / Year: 2013 Title: Surface for catalysis by poliovirus RNA-dependent RNA polymerase. Authors: Jing Wang / John M Lyle / Esther Bullitt / Abstract: The poliovirus RNA-dependent RNA polymerase, 3Dpol, replicates the viral genomic RNA on the surface of virus-induced intracellular membranes. Macromolecular assemblies of 3Dpol form linear arrays of ...The poliovirus RNA-dependent RNA polymerase, 3Dpol, replicates the viral genomic RNA on the surface of virus-induced intracellular membranes. Macromolecular assemblies of 3Dpol form linear arrays of subunits that propagate along a strong protein-protein interaction called interface-I, as was observed in the crystal structure of wild-type poliovirus polymerase. These "filaments" recur with slight modifications in planar sheets and, with additional modifications that accommodate curvature, in helical tubes of the polymerase, by packing filaments together via a second set of interactions. Periodic variations of subunit orientations within 3Dpol tubes give rise to "ghost reflections" in diffraction patterns computed from electron cryomicrographs of helical arrays. The ghost reflections reveal that polymerase tubes are formed by bundles of four to five interface-I filaments, which are then connected to the next bundle of filaments with a perturbation of interface interactions between bundles. While enzymatically inactive polymerase is also capable of oligomerization, much thinner tubes that lack interface-I interactions between adjacent subunits are formed, suggesting that long-range allostery produces conformational changes that extend from the active site to the protein-protein interface. Macromolecular assemblies of poliovirus polymerase show repeated use of flexible interface interactions for polymerase lattice formation, suggesting that adaptability of polymerase-polymerase interactions facilitates RNA replication. In addition, the presence of a positively charged groove identified in polymerase arrays may help position and stabilize the RNA template during replication. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2270.map.gz | 80 MB | EMDB map data format | |
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Header (meta data) | emd-2270-v30.xml emd-2270.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | EMD-2270.png | 273.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2270 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2270 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2270.map.gz / Format: CCP4 / Size: 115.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Helical reconstruction of wild-type poliovirus polymerase tubes n,l (1,0): -32, 5 n,l (0,1): 6, 30 Map has 2-fold symmetry around the helical axis. t= 170, u= 495 (l = 170n + 495m) dphi = 123.636364, dz = 6.071919 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Average reconstruction of poliovirus polymerase tubes
Entire | Name: Average reconstruction of poliovirus polymerase tubes |
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Components |
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-Supramolecule #1000: Average reconstruction of poliovirus polymerase tubes
Supramolecule | Name: Average reconstruction of poliovirus polymerase tubes / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 17.4 MDa |
-Macromolecule #1: polymerase
Macromolecule | Name: polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 331 / Recombinant expression: Yes |
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Source (natural) | Organism: Human poliovirus 1 Mahoney |
Molecular weight | Theoretical: 52.5 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pT5T-3D |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Grid | Details: Quantifoil |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder: LN2 cooled / Specimen holder model: OTHER |
Date | Jan 1, 2011 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 6.1 Å Applied symmetry - Helical parameters - Δ&Phi: 67.5 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Software - Name: MRC, EMIP, Chimera |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL |