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- EMDB-2133: The Structure of Lactococcal Phage TP901-1 by electron microscopy... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2133 | |||||||||
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Title | The Structure of Lactococcal Phage TP901-1 by electron microscopy: the capsid | |||||||||
![]() | Icosahedral reconstruction of the capsid of the phage TP901-1 | |||||||||
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![]() | EM / capsid / icosahedral / tp901 / lactococcal phage | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.0 Å | |||||||||
![]() | Bebeacua C / Lai L / Skovgaard Vegge C / Brondsted L / van Heel M / Veesler D / Cambillau C | |||||||||
![]() | ![]() Title: Visualizing a complete Siphoviridae member by single-particle electron microscopy: the structure of lactococcal phage TP901-1. Authors: Cecilia Bebeacua / Livia Lai / Christina Skovgaard Vegge / Lone Brøndsted / Marin van Heel / David Veesler / Christian Cambillau / ![]() Abstract: Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive ...Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive bacterium Lactococcus lactis using receptor-binding proteins anchored to the host adsorption apparatus (baseplate). Crystallographic and electron microscopy (EM) studies have shed light on the distinct adsorption strategies used by phages of these two families, suggesting that they might also rely on different infection mechanisms. Here, we report electron microscopy reconstructions of the whole phage TP901-1 (P335 species) and propose a composite EM model of this gigantic molecular machine. Our results suggest conservation of structural proteins among tailed phages and add to the growing body of evidence pointing to a common evolutionary origin for these virions. Finally, we propose that host adsorption apparatus architectures have evolved in correlation with the nature of the receptors used during infection. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.5 KB 10.5 KB | Display Display | ![]() |
Images | ![]() | 732.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Icosahedral reconstruction of the capsid of the phage TP901-1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Icosahedral capsid of the lactococcal phage TP901-1
Entire | Name: Icosahedral capsid of the lactococcal phage TP901-1 |
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Components |
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-Supramolecule #1000: Icosahedral capsid of the lactococcal phage TP901-1
Supramolecule | Name: Icosahedral capsid of the lactococcal phage TP901-1 / type: sample / ID: 1000 Details: The sample corresponded to the full phage but only the capsid particles were selected. Oligomeric state: Icosahedral / Number unique components: 1 |
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Molecular weight | Experimental: 13 MDa / Theoretical: 13 MDa |
-Supramolecule #1: Lactococcus phage TP901-1
Supramolecule | Name: Lactococcus phage TP901-1 / type: virus / ID: 1 Details: The sample contained the full phages with tail and baseplate. Only the capsids were selected. NCBI-ID: 35345 / Sci species name: Lactococcus phage TP901-1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Molecular weight | Experimental: 13 MDa / Theoretical: 13 MDa |
Virus shell | Shell ID: 1 / Diameter: 600 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Details: SM buffer (100 mM sodium chloride, 10 mM magnesium sulfate, 50 mM Tris [pH 7.5], and 0.01% [wt/vol] gelatin) |
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Grid | Details: Quantifoil grids were glow discharged for 20 seconds |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 2 seconds before plunging |
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Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Temperature | Min: 80 K / Max: 105 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 130,000 times magnification. |
Specialist optics | Energy filter - Name: FEI |
Date | Jun 1, 2008 |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Number real images: 200 / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Details | The particles were submitted to single-particle analysis with icosahedral symmetry using IMAGIC-V |
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CTF correction | Details: Images |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 1500 |
Final angle assignment | Details: ICOSAHEDRAL |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | Protocol: Rigid body. Manually fitted 60 copies of the hexamer of HK97. Every hexamer was refined using Chimera. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 10 |