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Yorodumi- EMDB-9010: Structure of bacteriophage P22 with trans-envelope channel in the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9010 | |||||||||
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Title | Structure of bacteriophage P22 with trans-envelope channel in the Salmonella cell wall | |||||||||
Map data | Bacteriophage P22 with trans-envelope channel in the Salmonella cell wall | |||||||||
Sample |
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Biological species | Enterobacteria phage P22 (virus) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 29.0 Å | |||||||||
Authors | Liu J / Molineux IJ / Wang CY | |||||||||
Citation | Journal: Nat Microbiol / Year: 2019 Title: Structural dynamics of bacteriophage P22 infection initiation revealed by cryo-electron tomography. Authors: Chunyan Wang / Jiagang Tu / Jun Liu / Ian J Molineux / Abstract: For successful infection, bacteriophages must overcome multiple barriers to transport their genome and proteins across the bacterial cell envelope. We use cryo-electron tomography to study the ...For successful infection, bacteriophages must overcome multiple barriers to transport their genome and proteins across the bacterial cell envelope. We use cryo-electron tomography to study the infection initiation of phage P22 in Salmonella enterica serovar Typhimurium, revealing how a channel forms to allow genome translocation into the cytoplasm. Our results show free phages that initially attach obliquely to the cell through interactions between the O antigen and two of the six tailspikes; the tail needle also abuts the cell surface. The virion then orients perpendicularly and the needle penetrates the outer membrane. The needle is released and the internal head protein gp7* is ejected and assembles into an extracellular channel that extends from the gp10 baseplate to the cell surface. A second protein, gp20, is ejected and assembles into a structure that extends the extracellular channel across the outer membrane into the periplasm. Insertion of the third ejected protein, gp16, into the cytoplasmic membrane probably completes the overall trans-envelope channel into the cytoplasm. Construction of a trans-envelope channel is an essential step during infection of Gram-negative bacteria by all short-tailed phages, because such virions cannot directly deliver their genome into the cell cytoplasm. | |||||||||
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_9010.map.gz | 164 MB | EMDB map data format | |
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Header (meta data) | emd-9010-v30.xml emd-9010.xml | 7.8 KB 7.8 KB | Display Display | EMDB header |
Images | emd_9010.png | 100.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9010 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9010 | HTTPS FTP |
-Validation report
Summary document | emd_9010_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_9010_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_9010_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9010 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9010 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9010.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bacteriophage P22 with trans-envelope channel in the Salmonella cell wall | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.5 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 : Structure of bacteriohage P22 with trans-envelope channel in the ...
Entire | Name: Structure of bacteriohage P22 with trans-envelope channel in the Salmonella cell wall |
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Components |
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-Supramolecule #1: Structure of bacteriohage P22 with trans-envelope channel in the ...
Supramolecule | Name: Structure of bacteriohage P22 with trans-envelope channel in the Salmonella cell wall type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Enterobacteria phage P22 (virus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 6002 |
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Extraction | Number tomograms: 316 / Number images used: 38000 |
Final angle assignment | Type: ANGULAR RECONSTITUTION |