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Yorodumi- PDB-8tvu: In situ cryo-EM structure of bacteriophage P22 portal protein: he... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tvu | ||||||
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Title | In situ cryo-EM structure of bacteriophage P22 portal protein: head-to-tail protein complex at 3.0A resolution | ||||||
Components |
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Keywords | VIRAL PROTEIN / phage / bacteriophage / portal protein / head-to-tail protein / gene product 1 (gp1) / gene product 4 (gp4 / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information viral DNA genome packaging, headful / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / virus tail / virion assembly / hydrolase activity Similarity search - Function | ||||||
Biological species | Salmonella phage P22 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Iglesias, S.M. / Cingolani, G. / Feng-Hou, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Mol Biol / Year: 2023 Title: Molecular Architecture of Salmonella Typhimurium Virus P22 Genome Ejection Machinery. Authors: Stephano M Iglesias / Ravi K Lokareddy / Ruoyu Yang / Fenglin Li / Daniel P Yeggoni / Chun-Feng David Hou / Makayla N Leroux / Juliana R Cortines / Justin C Leavitt / Mary Bird / Sherwood R ...Authors: Stephano M Iglesias / Ravi K Lokareddy / Ruoyu Yang / Fenglin Li / Daniel P Yeggoni / Chun-Feng David Hou / Makayla N Leroux / Juliana R Cortines / Justin C Leavitt / Mary Bird / Sherwood R Casjens / Simon White / Carolyn M Teschke / Gino Cingolani / Abstract: Bacteriophage P22 is a prototypical member of the Podoviridae superfamily. Since its discovery in 1952, P22 has become a paradigm for phage transduction and a model for icosahedral viral capsid ...Bacteriophage P22 is a prototypical member of the Podoviridae superfamily. Since its discovery in 1952, P22 has become a paradigm for phage transduction and a model for icosahedral viral capsid assembly. Here, we describe the complete architecture of the P22 tail apparatus (gp1, gp4, gp10, gp9, and gp26) and the potential location and organization of P22 ejection proteins (gp7, gp20, and gp16), determined using cryo-EM localized reconstruction, genetic knockouts, and biochemical analysis. We found that the tail apparatus exists in two equivalent conformations, rotated by ∼6° relative to the capsid. Portal protomers make unique contacts with coat subunits in both conformations, explaining the 12:5 symmetry mismatch. The tail assembles around the hexameric tail hub (gp10), which folds into an interrupted β-propeller characterized by an apical insertion domain. The tail hub connects proximally to the dodecameric portal protein and head-to-tail adapter (gp4), distally to the trimeric tail needle (gp26), and laterally to six trimeric tailspikes (gp9) that attach asymmetrically to gp10 insertion domain. Cryo-EM analysis of P22 mutants lacking the ejection proteins gp7 or gp20 and biochemical analysis of purified recombinant proteins suggest that gp7 and gp20 form a molecular complex associated with the tail apparatus via the portal protein barrel. We identified a putative signal transduction pathway from the tailspike to the tail needle, mediated by three flexible loops in the tail hub, that explains how lipopolysaccharide (LPS) is sufficient to trigger the ejection of the P22 DNA in vitro. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tvu.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8tvu.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8tvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/8tvu ftp://data.pdbj.org/pub/pdb/validation_reports/tv/8tvu | HTTPS FTP |
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-Related structure data
Related structure data | 41651MC 8tvrC 8u10C 8u11C 8u1oC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 82829.375 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26744 #2: Protein | Mass: 18044.959 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Salmonella phage P22 (virus) / References: UniProt: P26746 |
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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 |
-Sample preparation
Component | Name: Salmonella phage P22 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Salmonella phage P22 (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Salmonella enterica |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 29000 X / Calibrated magnification: 29000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2100 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.08 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
Image scans | Width: 11520 / Height: 8184 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C12 (12 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38151 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
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