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- EMDB-4730: Subtomogram average of MAC sheath and inner tube of P. luteoviola... -

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Basic information

Entry
Database: EMDB / ID: EMD-4730
TitleSubtomogram average of MAC sheath and inner tube of P. luteoviolacea Mif1 mutant
Map data
Sample
  • Complex: MAC array
Biological speciesPseudoalteromonas luteoviolacea (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 18.0 Å
AuthorsEisenstein F / Medeiros J / Pilhofer M
CitationJournal: Elife / Year: 2019
Title: A contractile injection system stimulates tubeworm metamorphosis by translocating a proteinaceous effector.
Authors: Charles F Ericson / Fabian Eisenstein / João M Medeiros / Kyle E Malter / Giselle S Cavalcanti / Robert W Zeller / Dianne K Newman / Martin Pilhofer / Nicholas J Shikuma /
Abstract: The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe-animal interaction is ...The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe-animal interaction is critical for the life cycles of diverse marine animals, what types of biochemical cues from bacteria that induce metamorphosis has been a mystery. Metamorphosis of larvae of the tubeworm is induced by arrays of phage tail-like contractile injection systems, which are released by the bacterium . Here we identify the novel effector protein Mif1. By cryo-electron tomography imaging and functional assays, we observe Mif1 as cargo inside the tube lumen of the contractile injection system and show that the gene is required for inducing metamorphosis. Purified Mif1 is sufficient for triggering metamorphosis when electroporated into tubeworm larvae. Our results indicate that the delivery of protein effectors by contractile injection systems may orchestrate microbe-animal interactions in diverse contexts.
History
DepositionMar 26, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4730.png

Downloads & links

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Map

FileDownload / File: emd_4730.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.29 Å/pix.
x 80 pix.
= 343.2 Å		4.29 Å/pix.
x 80 pix.
= 343.2 Å		4.29 Å/pix.
x 80 pix.
= 343.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.4898567 - 4.831291
Average (Standard dev.)0.0046715457 (±0.7474824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 343.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.294.294.29
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z343.200343.200343.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-4.4904.8310.005

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Supplemental data

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Sample components

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Entire : MAC array

EntireName: MAC array
Components
  • Complex: MAC array

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Supramolecule #1: MAC array

SupramoleculeName: MAC array / type: complex / ID: 1 / Parent: 0 / Details: deltaMif1
Source (natural)Organism: Pseudoalteromonas luteoviolacea (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 13425
ExtractionNumber tomograms: 63 / Number images used: 37024
Final angle assignmentType: OTHER

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