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- PDB-6zih: Topological model of p2 virion baseplate in activated conformation -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zih | ||||||
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Title | Topological model of p2 virion baseplate in activated conformation | ||||||
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![]() | VIRAL PROTEIN / lactococcal siphophage p2 / baseplate / receptor-binding protein / Distal Tail protein / Tail-associated lysin | ||||||
Function / homology | ![]() symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 28.7 Å | ||||||
![]() | Spinelli, S. / Cambillau, C. / Goulet, A. | ||||||
![]() | ![]() Title: Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism. Authors: Silvia Spinelli / Denise Tremblay / Sylvain Moineau / Christian Cambillau / Adeline Goulet / ![]() ![]() Abstract: Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated ...Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the model siphophage for this viral genus. The baseplate of phage p2, which is used to recognize its host, was previously shown to display two conformations by X-ray crystallography, a rested state and an activated state ready to bind to the host. The baseplate became only activated and opened in the presence of Ca. However, such an activated state was not previously observed in the virion. Here, using nanobodies binding to the baseplate, we report on the negative staining electron microscopy structure of the activated form of the baseplate directly observed in the p2 virion, that is compatible with the activated baseplate crystal structure. Analyses of this new structure also established the presence of a second distal tail (Dit) hexamer as a component of the baseplate, the topology of which differs largely from the first one. We also observed an uncoupling between the baseplate activation and the tail tip protein (Tal) opening, suggesting an infection mechanism more complex than previously expected. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 276.8 KB | Display | ![]() |
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PDB format | ![]() | 203.2 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 725.5 KB | Display | ![]() |
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Full document | ![]() | 725.1 KB | Display | |
Data in XML | ![]() | 95.6 KB | Display | |
Data in CIF | ![]() | 151.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11226MC ![]() 6zigC ![]() 6zjjC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 34511.992 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 42883.266 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 28668.057 Da / Num. of mol.: 18 / 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: Lactococcus virus P2 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Lactococcus lactis |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE / Material: uranyl acetate |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Spirit / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI SPIRIT |
Electron gun | Electron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: OTHER |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 293 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 28.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2X53 Accession code: 2X53 / Source name: PDB / Type: experimental model |