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
Deposition
Jul 18, 2013
-
Header (metadata) release
Jul 31, 2013
-
Map release
Aug 7, 2013
-
Update
Sep 18, 2013
-
Current status
Sep 18, 2013
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_2419.map.gz / Format: CCP4 / Size: 21.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Reconstruction of the full Afp particle
Voxel size
X=Y=Z: 3.07 Å
Density
Contour Level
By AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum
-6.86292648 - 9.212231640000001
Average (Standard dev.)
0.0 (±1.0)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-60
-60
-200
Dimensions
120
120
400
Spacing
120
120
400
Cell
A: 368.4 Å / B: 368.4 Å / C: 1228.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
3.07
3.07
3.07
M x/y/z
120
120
400
origin x/y/z
0.000
0.000
0.000
length x/y/z
368.400
368.400
1228.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
-40
NX/NY/NZ
55
55
81
MAP C/R/S
1
2
3
start NC/NR/NS
-60
-60
-200
NC/NR/NS
120
120
400
D min/max/mean
-6.863
9.212
-0.000
-
Supplemental data
-
Sample components
-
Entire : Antifeeding prophage of Serratia entomophila
Entire
Name: Antifeeding prophage of Serratia entomophila
Components
Sample: Antifeeding prophage of Serratia entomophila
Protein or peptide: Antifeeding prophage
-
Supramolecule #1000: Antifeeding prophage of Serratia entomophila
Supramolecule
Name: Antifeeding prophage of Serratia entomophila / type: sample / ID: 1000 / Details: Afp particle produced from 18 ORF products / Number unique components: 1
-
Macromolecule #1: Antifeeding prophage
Macromolecule
Name: Antifeeding prophage / type: protein_or_peptide / ID: 1 / Name.synonym: Afp Details: Product of the expression of 18 ORF's of the pADAP plasmid of Serratia entomophila Number of copies: 1 / Recombinant expression: Yes
Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: HOMEMADE PLUNGER Method: Glow-discharge grid in amyl amine atmosphere Apply 5 ul sample, 4C, humidity 90% Blot Plunge
-
Electron microscopy
Microscope
FEI TECNAI 12
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: 113 / Bits/pixel: 16
Tilt angle min
0
Tilt angle max
0
Electron beam
Acceleration voltage: 120 kV / Electron source: LAB6
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi