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Open data
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Basic information
Entry | Database: PDB / ID: 9jyy | |||||||||||||||||||||
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Title | core proteins of mature T7 | |||||||||||||||||||||
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![]() | VIRAL PROTEIN / Complex | |||||||||||||||||||||
Function / homology | ![]() symbiont genome ejection through host cell envelope / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / peptidoglycan lytic transglycosylase activity / symbiont genome ejection through host cell envelope, short tail mechanism / peptidoglycan metabolic process / symbiont entry into host / T=7 icosahedral viral capsid / symbiont entry into host cell via disruption of host cell envelope / virion component ...symbiont genome ejection through host cell envelope / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / peptidoglycan lytic transglycosylase activity / symbiont genome ejection through host cell envelope, short tail mechanism / peptidoglycan metabolic process / symbiont entry into host / T=7 icosahedral viral capsid / symbiont entry into host cell via disruption of host cell envelope / virion component / killing of cells of another organism / hydrolase activity / defense response to bacterium / host cell plasma membrane / membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||||||||||||||
![]() | Liu, H.R. / Chen, W.Y. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational changes in and translocation of small proteins: insights into the ejection mechanism of podophages. Authors: Jing Zheng / Hao Xiao / Hao Pang / Li Wang / Jingdong Song / Wenyuan Chen / Lingpeng Cheng / Hongrong Liu / ![]() Abstract: Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope ...Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope channel for DNA ejection. Although the core proteins of bacteriophage T7 have been resolved at near-atomic resolution, the mechanisms of core proteins and DNA ejection remain to be fully elucidated. In this study, we provided improved structures of core proteins in mature T7 and the portal-tail complex in lipopolysaccharide-induced DNA-ejected T7 to resolutions of approximately 3 Å. Using these structures, we identified three small proteins, namely gp14, gp6.7, and gp7.3, and illustrated the conformational changes in and translocation of these proteins from the mature to DNA-ejected states. Our structures indicate that gp6.7, which participates in the assembly of the core and trans-envelope channel, is a core protein, and that gp7.3 serves as a structural scaffold to assist the assembly of the nozzle into the adaptor. IMPORTANCE: Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in ...IMPORTANCE: Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in the periplasmic tunnel form in the DNA-ejected T7 have been resolved previously. Here, we resolved the structures of two new structural proteins (gp6.7 and gp7.3) within mature T7 and receptor-induced DNA-ejected T7. The gp6.7 protein participates in the assembly of the core complex within mature T7 and the trans-envelope channel during T7 infection; therefore, gp6.7 is a core protein. Before T7 infection, gp7.3 plays a role in promoting the assembly of the nozzle into the adaptor. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 589 KB | Display | ![]() |
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Full document | ![]() | 793.8 KB | Display | |
Data in XML | ![]() | 219.6 KB | Display | |
Data in CIF | ![]() | 333.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 61909MC ![]() 9jyzC ![]() 9jz0C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 9354.512 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 20990.842 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 84454.008 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 144028.219 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03726, Lyases; Carbon-oxygen lyases; Acting on polysaccharides Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Escherichia phage T7 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45731 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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