+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5232 | |||||||||
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Title | Icosahedral P22 | |||||||||
Map data | icosahedral P22 | |||||||||
Sample |
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Keywords | icosahedral reconstruction / phage | |||||||||
Biological species | Enterobacteria phage P22 (virus) | |||||||||
Method | single particle reconstruction / cryo EM | |||||||||
Authors | Tang J / Lander G / Olia A / Li R / Casjens S / Prevelige P / Cingolani G / Baker TS / Johnson JE | |||||||||
Citation | Journal: Structure / Year: 2011 Title: Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22. Authors: Jinghua Tang / Gabriel C Lander / Adam S Olia / Rui Li / Sherwood Casjens / Peter Prevelige / Gino Cingolani / Timothy S Baker / John E Johnson / Abstract: The encapsidated genome in all double-strand DNA bacteriophages is packaged to liquid crystalline density through a unique vertex in the procapsid assembly intermediate, which has a portal protein ...The encapsidated genome in all double-strand DNA bacteriophages is packaged to liquid crystalline density through a unique vertex in the procapsid assembly intermediate, which has a portal protein dodecamer in place of five coat protein subunits. The portal orchestrates DNA packaging and exit, through a series of varying interactions with the scaffolding, terminase, and closure proteins. Here, we report an asymmetric cryoEM reconstruction of the entire P22 virion at 7.8 Å resolution. X-ray crystal structure models of the full-length portal and of the portal lacking 123 residues at the C terminus in complex with gene product 4 (Δ123portal-gp4) obtained by Olia et al. (2011) were fitted into this reconstruction. The interpreted density map revealed that the 150 Å, coiled-coil, barrel portion of the portal entraps the last DNA to be packaged and suggests a mechanism for head-full DNA signaling and transient stabilization of the genome during addition of closure proteins. | |||||||||
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_5232.map.gz | 7 MB | EMDB map data format | |
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Header (meta data) | emd-5232-v30.xml emd-5232.xml | 7.2 KB 7.2 KB | Display Display | EMDB header |
Images | emd_5232_1.jpg | 128.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5232 | HTTPS FTP |
-Validation report
Summary document | emd_5232_validation.pdf.gz | 77.3 KB | Display | EMDB validaton report |
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Full document | emd_5232_full_validation.pdf.gz | 76.4 KB | Display | |
Data in XML | emd_5232_validation.xml.gz | 498 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5232 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5232 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5232.map.gz / Format: CCP4 / Size: 29.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | icosahedral P22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : P22 virus
Entire | Name: P22 virus |
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Components |
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-Supramolecule #1000: P22 virus
Supramolecule | Name: P22 virus / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Enterobacteria phage P22
Supramolecule | Name: Enterobacteria phage P22 / type: virus / ID: 1 / Name.synonym: p22 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: p22 |
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Host (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) synonym: BACTERIA(EUBACTERIA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Digitization - Sampling interval: 1.05 µm / Number real images: 2888 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |