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Yorodumi- EMDB-1207: Structure of the bacteriophage phi6 nucleocapsid suggests a mecha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1207 | |||||||||
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Title | Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. | |||||||||
Map data | Reconstruction of phi6 empty nucleocapsid | |||||||||
Sample |
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Biological species | Pseudomonas phage phi6 (bacteriophage) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Huiskonen JT / de Haas F / Bubeck D / Bamford DH / Fuller SD / Butcher SJ | |||||||||
Citation | Journal: Structure / Year: 2006 Title: Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. Authors: Juha T Huiskonen / Felix de Haas / Doryen Bubeck / Dennis H Bamford / Stephen D Fuller / Sarah J Butcher / Abstract: Bacteriophage phi6 is an enveloped dsRNA virus with a segmented genome. Phi6 specifically packages one copy of each of its three genome segments into a preassembled polymerase complex. This leads to ...Bacteriophage phi6 is an enveloped dsRNA virus with a segmented genome. Phi6 specifically packages one copy of each of its three genome segments into a preassembled polymerase complex. This leads to expansion of the polymerase complex, minus and plus strand RNA synthesis, and assembly of the nucleocapsid. The phi6 in vitro assembly and packaging system is a valuable model for dsRNA virus replication. The structure of the nucleocapsid at 7.5 A resolution presented here reveals the secondary structure of the two major capsid proteins. Asymmetric P1 dimers organize as an inner T = 1 shell, and P8 trimers organize as an outer T = 13 laevo shell. The organization of the P1 molecules in the unexpanded and expanded polymerase complex suggests that the expansion is accomplished by rigid body movements of the P1 monomers. This leads to exposure of new potential RNA binding surfaces to control the sequential packaging of the genome segments. | |||||||||
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_1207.map.gz | 25.2 MB | EMDB map data format | |
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Header (meta data) | emd-1207-v30.xml emd-1207.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | 1207.gif | 42.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1207 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1207 | HTTPS FTP |
-Validation report
Summary document | emd_1207_validation.pdf.gz | 317.9 KB | Display | EMDB validaton report |
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Full document | emd_1207_full_validation.pdf.gz | 317 KB | Display | |
Data in XML | emd_1207_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1207 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1207 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1207.map.gz / Format: CCP4 / Size: 39.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of phi6 empty nucleocapsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 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 : Bacteriophage phi6 nucleocapsid
Entire | Name: Bacteriophage phi6 nucleocapsid |
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Components |
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-Supramolecule #1000: Bacteriophage phi6 nucleocapsid
Supramolecule | Name: Bacteriophage phi6 nucleocapsid / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 22 MDa |
-Supramolecule #1: Pseudomonas phage phi6
Supramolecule | Name: Pseudomonas phage phi6 / type: virus / ID: 1 / Name.synonym: Bacteriophage phi6 / NCBI-ID: 10879 / Sci species name: Pseudomonas phage phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: Bacteriophage phi6 |
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Host (natural) | Organism: Pseudomonas syringae pv phaesolicola HB10Y / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Name: PC shell / Diameter: 485 Å / T number (triangulation number): 1 |
Virus shell | Shell ID: 2 / Name: NC shell / Diameter: 555 Å / T number (triangulation number): 13 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 93 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 37 / Bits/pixel: 12 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each particle, full CTF correction |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: P3DR Details: The map was calculated from empty particles lacking the genome Number images used: 1163 |