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- EMDB-1779: EM structure of bacteriophage SPP1 distal tail protein (GP 19.1):... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1779 | |||||||||
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Title | EM structure of bacteriophage SPP1 distal tail protein (GP 19.1): a baseplate hub paradigm in gram positive infecting phages | |||||||||
![]() | EM map of Dit (GP19.1) from SPP1 Bacteriophage | |||||||||
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![]() | Dit / GP 19.1 / SPP1 / Bacteriophage | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.5 Å | |||||||||
![]() | Veesler D / Robin G / Lichiere J / Auzat I / Tavares P / Bron P / Campanacci V / Cambillau C | |||||||||
![]() | ![]() Title: Crystal structure of bacteriophage SPP1 distal tail protein (gp19.1): a baseplate hub paradigm in gram-positive infecting phages. Authors: David Veesler / Gautier Robin / Julie Lichière / Isabelle Auzat / Paulo Tavares / Patrick Bron / Valérie Campanacci / Christian Cambillau / ![]() Abstract: Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most ...Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most orf products belonging to these regions. We report here the structure of the SPP1 distal tail protein (Dit, gp19.1). The combination of x-ray crystallography, EM, and light scattering established that Dit is a back-to-back dimer of hexamers. However, Dit fitting in the virion EM maps was only possible with a hexamer located between the tail-tube and the tail-tip. Structure comparison revealed high similarity between Dit and a central component of lactophage baseplates. Sequence similarity search expanded its relatedness to several phage proteins, suggesting that Dit is a docking platform for the tail adsorption apparatus in Siphoviridae infecting gram-positive bacteria and that its architecture is a paradigm for these hub proteins. Dit structural similarity extends also to non-contractile and contractile phage tail proteins (gpV(N) and XkdM) as well as to components of the bacterial type 6 secretion system, supporting an evolutionary connection between all these devices. | |||||||||
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 | ![]() | 7.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.4 KB 9.4 KB | Display Display | ![]() |
Images | ![]() | 95.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 211.5 KB | Display | ![]() |
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Full document | ![]() | 210.6 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EM map of Dit (GP19.1) from SPP1 Bacteriophage | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.19 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 : GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage
Entire | Name: GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage |
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Components |
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-Supramolecule #1000: GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage
Supramolecule | Name: GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Dodecameric / Number unique components: 1 |
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Molecular weight | Experimental: 325.629 KDa / Theoretical: 28.489 KDa Method: Molar mass and hydrodynamic radius determination by SEC, MALS,UV,QELS and RI. |
-Macromolecule #1: GP19.1
Macromolecule | Name: GP19.1 / type: protein_or_peptide / ID: 1 / Name.synonym: Dit / Number of copies: 12 / Oligomeric state: Dodecameric / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.010 mg/mL |
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Buffer | pH: 7.5 / Details: 10 mM HEPES, 150 mM NaCl |
Staining | Type: NEGATIVE Details: 3 microLitres of freshly prepared protein were applied on a glow-discharged carbon-coated grid. The excess of Dit solution was blotted and 4 microliters of 1% Uranyl- Acetate was applied ...Details: 3 microLitres of freshly prepared protein were applied on a glow-discharged carbon-coated grid. The excess of Dit solution was blotted and 4 microliters of 1% Uranyl- Acetate was applied twice on the grid and incubated for 1 min. Grids were then dried and kept in a desiccator cabinet until use |
Grid | Details: 400-Mesh Carbon-Coated Copper Grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | JEOL 2200FS |
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Specialist optics | Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Details | Low-dose imaging |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 10 µm / Number real images: 8 / Average electron dose: 18 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 45710 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: JEOL |
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Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC V / Number images used: 9027 |