+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31318 | ||||||||||||
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Title | LPS-treated empty bacteriophage T7 | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information virus tail, tube / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / viral DNA genome packaging / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Escherichia phage T7 (virus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | ||||||||||||
Authors | Liu HR / Chen WY | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structural changes in bacteriophage T7 upon receptor-induced genome ejection. Authors: Wenyuan Chen / Hao Xiao / Li Wang / Xurong Wang / Zhixue Tan / Zhen Han / Xiaowu Li / Fan Yang / Zhonghua Liu / Jingdong Song / Hongrong Liu / Lingpeng Cheng / Abstract: Many tailed bacteriophages assemble ejection proteins and a portal-tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal-tail channel ...Many tailed bacteriophages assemble ejection proteins and a portal-tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal-tail channel for the delivery of genomic DNA in cell infection. Here, we report the structure of the mature bacteriophage T7, including the ejection proteins, as well as the structures of the full and empty T7 particles in complex with their cell receptor lipopolysaccharide. Our near-atomic-resolution reconstruction shows that the ejection proteins in the mature T7 assemble into a core, which comprises a fourfold gene product 16 (gp16) ring, an eightfold gp15 ring, and a putative eightfold gp14 ring. The gp15 and gp16 are mainly composed of helix bundles, and gp16 harbors a lytic transglycosylase domain for degrading the bacterial peptidoglycan layer. When interacting with the lipopolysaccharide, the T7 tail nozzle opens. Six copies of gp14 anchor to the tail nozzle, extending the nozzle across the lipopolysaccharide lipid bilayer. The structures of gp15 and gp16 in the mature T7 suggest that they should undergo remarkable conformational changes to form the transenvelope channel. Hydrophobic α-helices were observed in gp16 but not in gp15, suggesting that gp15 forms the channel in the hydrophilic periplasm and gp16 forms the channel in the cytoplasmic membrane. | ||||||||||||
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_31318.map.gz | 473.5 MB | EMDB map data format | |
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Header (meta data) | emd-31318-v30.xml emd-31318.xml | 8.1 KB 8.1 KB | Display Display | EMDB header |
Images | emd_31318.png | 74 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31318 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31318 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31318.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.54 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 : Escherichia phage T7
Entire | Name: Escherichia phage T7 (virus) |
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Components |
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-Supramolecule #1: Escherichia phage T7
Supramolecule | Name: Escherichia phage T7 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10760 / Sci species name: Escherichia phage T7 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 23.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: COMMON LINE |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61862 |