+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5378 | |||||||||
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Title | The structure of PBCV-1 (icosahedrally averaged map) | |||||||||
Map data | Icosahedrally averaged cryo-EM electron density map of PBCV-1. | |||||||||
Sample |
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Keywords | Cell entry / minor protein / double jelly-roll | |||||||||
Biological species | Paramecium bursaria Chlorella virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.8 Å | |||||||||
Authors | Zhang XZ / Xiang Y / Dunigan DD / Klose T / Chipman PR / Etten JLV / Rossmann MG | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2011 Title: Three-dimensional structure and function of the Paramecium bursaria chlorella virus capsid. Authors: Xinzheng Zhang / Ye Xiang / David D Dunigan / Thomas Klose / Paul R Chipman / James L Van Etten / Michael G Rossmann / Abstract: A cryoelectron microscopy 8.5 Å resolution map of the 1,900 Å diameter, icosahedral, internally enveloped Paramecium bursaria chlorella virus was used to interpret structures of the virus at ...A cryoelectron microscopy 8.5 Å resolution map of the 1,900 Å diameter, icosahedral, internally enveloped Paramecium bursaria chlorella virus was used to interpret structures of the virus at initial stages of cell infection. A fivefold averaged map demonstrated that two minor capsid proteins involved in stabilizing the capsid are missing in the vicinity of the unique vertex. Reconstruction of the virus in the presence of host chlorella cell walls established that the spike at the unique vertex initiates binding to the cell wall, which results in the enveloped nucleocapsid moving closer to the cell. This process is concurrent with the release of the internal viral membrane that was linked to the capsid by many copies of a viral membrane protein in the mature infectous virus. Simultaneously, part of the trisymmetrons around the unique vertex disassemble, probably in part because two minor capsid proteins are absent, causing Paramecium bursaria chlorella virus and the cellular contents to merge, possibly as a result of enzyme(s) within the spike assembly. This may be one of only a few recordings of successive stages of a virus while infecting a eukaryotic host in pseudoatomic detail in three dimensions. | |||||||||
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_5378.map.gz | 473.2 MB | EMDB map data format | |
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Header (meta data) | emd-5378-v30.xml emd-5378.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_5378_1.jpg | 106.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5378 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5378 | HTTPS FTP |
-Validation report
Summary document | emd_5378_validation.pdf.gz | 79.3 KB | Display | EMDB validaton report |
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Full document | emd_5378_full_validation.pdf.gz | 78.4 KB | Display | |
Data in XML | emd_5378_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5378 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5378 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5378.map.gz / Format: CCP4 / Size: 500 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Icosahedrally averaged cryo-EM electron density map of PBCV-1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.84 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 : PBCV-1
Entire | Name: PBCV-1 (virus) |
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Components |
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-Supramolecule #1000: PBCV-1
Supramolecule | Name: PBCV-1 / type: sample / ID: 1000 / Number unique components: 8 |
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-Supramolecule #1: Paramecium bursaria Chlorella virus 1
Supramolecule | Name: Paramecium bursaria Chlorella virus 1 / type: virus / ID: 1 / Name.synonym: PBCV-1 / NCBI-ID: 10506 / Sci species name: Paramecium bursaria Chlorella virus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: PBCV-1 |
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Host (natural) | Organism: Chlorella variabilis (plant) / synonym: ALGAE |
Virus shell | Shell ID: 1 / Name: VP54 / Diameter: 1850 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 / Details: BBM |
Grid | Details: 200 mesh grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 174 K / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Temperature | Average: 175 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 250,000 times magnification |
Image recording | Category: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 6.75 µm / Number real images: 800 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 33065 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder: Single tilt holder / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 17016 |