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- EMDB-2544: Electron cryo-microscopy subtomogram average of a contracted cont... -

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Basic information

Entry
Database: EMDB / ID: EMD-2544
TitleElectron cryo-microscopy subtomogram average of a contracted contractile structure in a MAC array
Map dataSubtomogram average of a contracted contractile structure in a MAC array
Sample
  • Sample: Culture of Pseudoalteromonas violacea cells
  • Organelle or cellular component: Contracted contractile structure in a MAC array
Keywordsmetamorphosis / contractile / tubeworm / phage tail / extended / MAC
Biological speciesPseudoalteromonas luteoviolacea (bacteria)
Methodsubtomogram averaging / cryo EM
AuthorsShikuma NJ / Pilhofer M / Weiss GL / Hadfield MG / Jensen GJ / Newman DK
CitationJournal: Science / Year: 2014
Title: Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures.
Authors: Nicholas J Shikuma / Martin Pilhofer / Gregor L Weiss / Michael G Hadfield / Grant J Jensen / Dianne K Newman /
Abstract: Many benthic marine animal populations are established and maintained by free-swimming larvae that recognize cues from surface-bound bacteria to settle and metamorphose. Larvae of the tubeworm ...Many benthic marine animal populations are established and maintained by free-swimming larvae that recognize cues from surface-bound bacteria to settle and metamorphose. Larvae of the tubeworm Hydroides elegans, an important biofouling agent, require contact with surface-bound bacteria to undergo metamorphosis; however, the mechanisms that underpin this microbially mediated developmental transition have been enigmatic. Here, we show that a marine bacterium, Pseudoalteromonas luteoviolacea, produces arrays of phage tail-like structures that trigger metamorphosis of H. elegans. These arrays comprise about 100 contractile structures with outward-facing baseplates, linked by tail fibers and a dynamic hexagonal net. Not only do these arrays suggest a novel form of bacterium-animal interaction, they provide an entry point to understanding how marine biofilms can trigger animal development.
History
DepositionDec 31, 2013-
Header (metadata) releaseJan 15, 2014-
Map releaseFeb 12, 2014-
UpdateFeb 12, 2014-
Current statusFeb 12, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 127
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 127
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_2544.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of a contracted contractile structure in a MAC array
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
16.8 Å/pix.
x 65 pix.
= 1092. Å		16.8 Å/pix.
x 65 pix.
= 1092. Å		16.8 Å/pix.
x 65 pix.
= 1092. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 16.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 127.0 / Movie #1: 127
Minimum - Maximum22.141006470000001 - 226.5
Average (Standard dev.)115.221542360000001 (±11.83436584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions656565
Spacing656565
CellA=B=C: 1092.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z16.816.816.8
M x/y/z656565
origin x/y/z0.0000.0000.000
length x/y/z1092.0001092.0001092.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS656565
D min/max/mean22.141226.500115.222

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Supplemental data

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Sample components

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Entire : Culture of Pseudoalteromonas violacea cells

EntireName: Culture of Pseudoalteromonas violacea cells
Components
  • Sample: Culture of Pseudoalteromonas violacea cells
  • Organelle or cellular component: Contracted contractile structure in a MAC array

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Supramolecule #1000: Culture of Pseudoalteromonas violacea cells

SupramoleculeName: Culture of Pseudoalteromonas violacea cells / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Contracted contractile structure in a MAC array

SupramoleculeName: Contracted contractile structure in a MAC array / type: organelle_or_cellular_component / ID: 1 / Oligomeric state: Structure is part of a MAC array / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Pseudoalteromonas luteoviolacea (bacteria) / Organelle: MAC array / Location in cell: cytoplasmic and extracellular

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

GridDetails: Quantifoil
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF
DateJul 12, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsPEET
Final reconstructionAlgorithm: OTHER / Software - Name: ETOMO / Number subtomograms used: 25

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