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- EMDB-4783: Composite map of an entire contractile injection device : the ant... -

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Basic information

Entry
Database: EMDB / ID: EMD-4783
TitleComposite map of an entire contractile injection device : the anti-feeding prophage (AFP)
Map dataComposite map of the full anti-feeding prophage (AFP) contractile injection device. This map was assembled from individual maps of cap, trunk, baseplate and needle (see related deposited maps)
Sample
  • Complex: Composite map of an entire contractile injection device : the anti-feeding prophage (AFP)
Biological speciesSerratia entomophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDesfosses A
CitationJournal: Nat Microbiol / Year: 2019
Title: Atomic structures of an entire contractile injection system in both the extended and contracted states.
Authors: Ambroise Desfosses / Hariprasad Venugopal / Tapan Joshi / Jan Felix / Matthew Jessop / Hyengseop Jeong / Jaekyung Hyun / J Bernard Heymann / Mark R H Hurst / Irina Gutsche / Alok K Mitra /
Abstract: Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, ...Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, bacterial type six secretion systems and R-pyocins is rapidly increasing, structural information on the contraction of bacterial phage-like protein-translocation structures directed towards eukaryotic hosts is scarce. Here, we characterize the antifeeding prophage AFP from Serratia entomophila by cryo-electron microscopy. We present the high-resolution structure of the entire AFP particle in the extended state, trace 11 protein chains de novo from the apical cap to the needle tip, describe localization variants and perform specific structural comparisons with related systems. We analyse inter-subunit interactions and highlight their universal conservation within contractile injection systems while revealing the specificities of AFP. Furthermore, we provide the structure of the AFP sheath-baseplate complex in a contracted state. This study reveals atomic details of interaction networks that accompany and define the contraction mechanism of toxin-delivery tailocins, offering a comprehensive framework for understanding their mode of action and for their possible adaptation as biocontrol agents.
History
DepositionApr 7, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseApr 17, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4783.png

Downloads & links

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Map

FileDownload / File: emd_4783.map.gz / Format: CCP4 / Size: 196.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the full anti-feeding prophage (AFP) contractile injection device. This map was assembled from individual maps of cap, trunk, baseplate and needle (see related deposited maps)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.3022376 - 0.47395718
Average (Standard dev.)0.0012110935 (±0.02485022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-448
Dimensions240240896
Spacing240240896
CellA: 324.0 Å / B: 324.0 Å / C: 1209.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z240240896
origin x/y/z0.0000.0000.000
length x/y/z324.000324.0001209.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-120-120-448
NC/NR/NS240240896
D min/max/mean-0.3020.4740.001

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Supplemental data

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Sample components

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Entire : Composite map of an entire contractile injection device : the ant...

EntireName: Composite map of an entire contractile injection device : the anti-feeding prophage (AFP)
Components
  • Complex: Composite map of an entire contractile injection device : the anti-feeding prophage (AFP)

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Supramolecule #1: Composite map of an entire contractile injection device : the ant...

SupramoleculeName: Composite map of an entire contractile injection device : the anti-feeding prophage (AFP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Details: This map was assembled from individual maps of cap, trunk, baseplate and needle (see related deposited maps)
Source (natural)Organism: Serratia entomophila (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 10.215 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 30858

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