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Yorodumi- EMDB-2423: 3-dimensional structure of the toxin-delivery particle antifeedin... -
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-Basic information
Entry | Database: EMDB / ID: EMD-2423 | |||||||||
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Title | 3-dimensional structure of the toxin-delivery particle antifeeding prophage of Serratia entomophila | |||||||||
Map data | Reconstruction of the Afp tube-baseplate complex | |||||||||
Sample |
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Keywords | tube-baseplate complex / tailocin / type VI secretion system / helical sheath / phage tail-like | |||||||||
Biological species | Serratia entomophila (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Heymann JB / Bartho JD / Rybakova D / Venugopal HP / Winkler DC / Sen A / Hurst MRH / Mitra AK | |||||||||
Citation | Journal: J Biol Chem / Year: 2013 Title: Three-dimensional structure of the toxin-delivery particle antifeeding prophage of Serratia entomophila. Authors: J Bernard Heymann / Joseph D Bartho / Daria Rybakova / Hari P Venugopal / Dennis C Winkler / Anindito Sen / Mark R H Hurst / Alok K Mitra / Abstract: The Serratia entomophila antifeeding prophage (Afp) is a bullet-shaped toxin-delivery apparatus similar to the R-pyocins of Pseudomonas aeruginosa. Morphologically it resembles the sheathed tail of ...The Serratia entomophila antifeeding prophage (Afp) is a bullet-shaped toxin-delivery apparatus similar to the R-pyocins of Pseudomonas aeruginosa. Morphologically it resembles the sheathed tail of bacteriophages such as T4, including a baseplate at one end. It also shares features with the type VI secretion systems. Cryo-electron micrographs of tilted Afp specimens (up to 60 degrees) were analyzed to determine the correct cyclic symmetry to overcome the limitation imposed by exclusively side views in nominally untilted specimens. An asymmetric reconstruction shows clear 6-fold cyclic symmetry contrary to a previous conclusion of 4-fold symmetry based on analysis of only the preferred side views (Sen, A., Rybakova, D., Hurst, M. R., and Mitra, A. K. (2010) J. Bacteriol. 192, 4522-4525). Electron tomography of negatively stained Afp revealed right-handed helical striations in many of the particles, establishing the correct hand. Higher quality micrographs of untilted specimens were processed to produce a reconstruction at 2.0-nm resolution with imposed 6-fold symmetry. The helical parameters of the sheath were determined to be 8.14 nm for the subunit rise along and 40.5° for the rotation angle around the helix. The sheath is similar to that of the T4 phage tail but with a different arrangement of the subdomain of the polymerizing sheath protein(s). The central tube is similar to the diameter and axial width of the Hcp1 hexamer of P. aeruginosa type VI secretion system. The tube extends through the baseplate into a needle resembling the "puncture device" of the T4 tail. The tube contains density that may be the toxin and/or a length-determining protein. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2423.map.gz | 15.3 MB | EMDB map data format | |
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Header (meta data) | emd-2423-v30.xml emd-2423.xml | 9 KB 9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_2423_fsc.xml | 3.6 KB | Display | FSC data file |
Images | emd_2423.png | 133.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2423 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2423 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2423.map.gz / Format: CCP4 / Size: 16.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the Afp tube-baseplate complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tube-baseplate complex of the antifeeding prophage of Serratia en...
Entire | Name: Tube-baseplate complex of the antifeeding prophage of Serratia entomophila |
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Components |
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-Supramolecule #1000: Tube-baseplate complex of the antifeeding prophage of Serratia en...
Supramolecule | Name: Tube-baseplate complex of the antifeeding prophage of Serratia entomophila type: sample / ID: 1000 Details: Tube-baseplate complex produced from 15 ORF products Number unique components: 1 |
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-Macromolecule #1: Antifeeding prophage tube-baseplate complex
Macromolecule | Name: Antifeeding prophage tube-baseplate complex / type: protein_or_peptide / ID: 1 / Name.synonym: TBC Details: Product of the expression of 15 ORF's of the pADAP plasmid of Serratia entomophila Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Serratia entomophila (bacteria) |
Recombinant expression | Organism: Escherichia coli str. K-12 substr. DH10B (bacteria) Recombinant plasmid: pAF1-15 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 25 mM TBS, 130 mM NaCl |
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Staining | Type: NEGATIVE / Details: 2% Uranyl acetate |
Grid | Details: Carbon film |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 50364 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.3 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: OTHER |
Date | Feb 11, 2013 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Number real images: 75 / Bits/pixel: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |