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- EMDB-4948: Cryo electron tomogram of Metamorphosis associated contractile ar... -

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Basic information

Entry
Database: EMDB / ID: EMD-4948
TitleCryo electron tomogram of Metamorphosis associated contractile array isolated from P. luteoviolacea deltaPne1
Map dataTomogram of MAC array isolated from P. luteoviolacea HI1 delta pne1
Sample
  • Complex: Metamorphosis associated contractile array (MAC array)
Biological speciesPseudoalteromonas luteoviolacea (bacteria)
Methodelectron tomography / cryo EM
AuthorsEisenstein F / Pilhofer M
Funding support2 items
OrganizationGrant numberCountry
European Research Council
Swiss National Science Foundation
CitationJournal: Cell Rep / Year: 2019
Title: A Bacterial Phage Tail-like Structure Kills Eukaryotic Cells by Injecting a Nuclease Effector.
Authors: Iara Rocchi / Charles F Ericson / Kyle E Malter / Sahar Zargar / Fabian Eisenstein / Martin Pilhofer / Sinem Beyhan / Nicholas J Shikuma /
Abstract: Many bacteria interact with target organisms using syringe-like structures called contractile injection systems (CISs). CISs structurally resemble headless bacteriophages and share evolutionarily ...Many bacteria interact with target organisms using syringe-like structures called contractile injection systems (CISs). CISs structurally resemble headless bacteriophages and share evolutionarily related proteins such as the tail tube, sheath, and baseplate complex. In many cases, CISs mediate trans-kingdom interactions between bacteria and eukaryotes by delivering effectors to target cells. However, the specific effectors and their modes of action are often unknown. Here, we establish an ex vivo model to study an extracellular CIS (eCIS) called metamorphosis-associated contractile structures (MACs) that target eukaryotic cells. MACs kill two eukaryotic cell lines, fall armyworm Sf9 cells and J774A.1 murine macrophage cells, by translocating an effector termed Pne1. Before the identification of Pne1, no CIS effector exhibiting nuclease activity against eukaryotic cells had been described. Our results define a new mechanism of CIS-mediated bacteria-eukaryote interaction and are a step toward developing CISs as novel delivery systems for eukaryotic hosts.
History
DepositionMay 9, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateJul 24, 2019-
Current statusJul 24, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_4948.png

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Map

FileDownload / File: emd_4948.map.gz / Format: CCP4 / Size: 181.8 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomogram of MAC array isolated from P. luteoviolacea HI1 delta pne1
Voxel sizeX=Y=Z: 10.88 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)21.456613999999998 (±5.5781446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1616107
Dimensions928960214
Spacing960928214
CellA: 10444.8 Å / B: 10096.64 Å / C: 2328.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z10.8810.8810.88
M x/y/z960928214
origin x/y/z0.0000.0000.000
length x/y/z10444.80010096.6402328.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS16-16107
NC/NR/NS960928214
D min/max/mean-128.000127.00021.457

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Supplemental data

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Sample components

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Entire : Metamorphosis associated contractile array (MAC array)

EntireName: Metamorphosis associated contractile array (MAC array)
Components
  • Complex: Metamorphosis associated contractile array (MAC array)

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Supramolecule #1: Metamorphosis associated contractile array (MAC array)

SupramoleculeName: Metamorphosis associated contractile array (MAC array)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudoalteromonas luteoviolacea (bacteria) / Strain: HI1 deltaPne1

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cytodiagnostics / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61

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