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Yorodumi- PDB-6zih: Topological model of p2 virion baseplate in activated conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zih | ||||||
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Title | Topological model of p2 virion baseplate in activated conformation | ||||||
Components |
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Keywords | VIRAL PROTEIN / lactococcal siphophage p2 / baseplate / receptor-binding protein / Distal Tail protein / Tail-associated lysin | ||||||
Function / homology | Function and homology information 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 | Lactococcus phage p2 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 28.7 Å | ||||||
Authors | Spinelli, S. / Cambillau, C. / Goulet, A. | ||||||
Citation | Journal: Viruses / Year: 2020 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zih.cif.gz | 276.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zih.ent.gz | 203.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zih_validation.pdf.gz | 725.5 KB | Display | wwPDB validaton report |
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Full document | 6zih_full_validation.pdf.gz | 725.1 KB | Display | |
Data in XML | 6zih_validation.xml.gz | 95.6 KB | Display | |
Data in CIF | 6zih_validation.cif.gz | 151.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/6zih ftp://data.pdbj.org/pub/pdb/validation_reports/zi/6zih | HTTPS FTP |
-Related structure data
Related structure data | 11226MC 6zigC 6zjjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 34511.992 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage p2 (virus) / References: UniProt: D3WAD3 #2: Protein | Mass: 42883.266 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage p2 (virus) / References: UniProt: D3KFX4 #3: Protein | Mass: 28668.057 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage p2 (virus) / References: UniProt: Q71AW2 |
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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: Lactococcus virus P2 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Lactococcus virus P2 |
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 |
-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 |
-Processing
EM software |
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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 |