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Yorodumi- EMDB-2545: Electron cryo-microscopy subtomogram average of a hexagon vertex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2545 | |||||||||
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Title | Electron cryo-microscopy subtomogram average of a hexagon vertex in a MAC array | |||||||||
Map data | Electron cryo-microscopy subtomogram average of a hexagon vertex in a MAC array | |||||||||
Sample |
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Keywords | metamorphosis / contractile / tubeworm / phage tail / extended / MAC | |||||||||
Biological species | Pseudoalteromonas luteoviolacea (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Shikuma NJ / Pilhofer M / Weiss GL / Hadfield MG / Jensen GJ / Newman DK | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2545.map.gz | 536.9 KB | EMDB map data format | |
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Header (meta data) | emd-2545-v30.xml emd-2545.xml | 7.7 KB 7.7 KB | Display Display | EMDB header |
Images | PastedGraphic-8.tiff | 303.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2545 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2545 | HTTPS FTP |
-Validation report
Summary document | emd_2545_validation.pdf.gz | 267.5 KB | Display | EMDB validaton report |
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Full document | emd_2545_full_validation.pdf.gz | 266.6 KB | Display | |
Data in XML | emd_2545_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2545 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2545 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2545.map.gz / Format: CCP4 / Size: 635.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Electron cryo-microscopy subtomogram average of a hexagon vertex in a MAC array | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 16.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Culture of Pseudoalteromonas violacea cells
Entire | Name: Culture of Pseudoalteromonas violacea cells |
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Components |
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-Supramolecule #1000: Culture of Pseudoalteromonas violacea cells
Supramolecule | Name: Culture of Pseudoalteromonas violacea cells / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Hexagon vertex in a MAC array
Supramolecule | Name: Hexagon vertex 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 |
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Source (natural) | Organism: Pseudoalteromonas luteoviolacea (bacteria) / Organelle: MAC array / Location in cell: cytoplasmic and extracellular |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Grid | Details: Quantifoil |
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Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Specialist optics | Energy filter - Name: GIF |
Date | Jul 12, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | PEET |
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Final reconstruction | Algorithm: OTHER / Software - Name: ETOMO / Number subtomograms used: 60 |