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- PDB-8u11: In situ cryo-EM structure of bacteriophage P22 gp1:gp5:gp4: gp10:... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8u11 | ||||||
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Title | In situ cryo-EM structure of bacteriophage P22 gp1:gp5:gp4: gp10: gp9 N-term complex in conformation 2 at 3.1A resolution | ||||||
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![]() | VIRAL PROTEIN / phage / bacteriophage / tail spike protein / TSP / gene product 9 (gp9) / Packaged DNA stabilization protein / gene product 10 (gp10) / STRUCTURAL PROTEIN / head-to-tail protein / gene product 4 (gp4) / Tail hub protein / gene product (1) / Portal protein / Coat protein / Major capsid protein / gene product 5 (gp5) | ||||||
Function / homology | ![]() viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral procapsid maturation ...viral DNA genome packaging, headful / endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral procapsid maturation / viral DNA genome packaging / virus tail / symbiont entry into host / T=7 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / virion assembly / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / viral capsid / hydrolase activity / virion attachment to host cell / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Iglesias, S. / Feng-Hou, C. / Cingolani, G. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 336.5 KB | Display | |
Data in CIF | ![]() | 573.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 41792MC ![]() 8tvrC ![]() 8tvuC ![]() 8u10C ![]() 8u1oC 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: 52512.020 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 71923.523 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 82829.375 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 18044.959 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 46795.613 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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: Salmonella phage P22 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
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 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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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: 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 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17944 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.42 Å2 | ||||||||||||||||||||||||
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