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Yorodumi- EMDB-13730: Cryo-electron tomography of an attached epibiotic cell of Ca. Abs... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13730 | |||||||||
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Title | Cryo-electron tomography of an attached epibiotic cell of Ca. Absconditicoccus predator | |||||||||
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Sample |
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Keywords | Patescibacteria / bacterium / UNKNOWN FUNCTION | |||||||||
Biological species | bacterium (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Gaisin V / Pilhofer M | |||||||||
Funding support | European Union, 2 items
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Citation | Journal: Environ Microbiol / Year: 2022 Title: Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'. Authors: Michail M Yakimov / Alexander Y Merkel / Vasil A Gaisin / Martin Pilhofer / Enzo Messina / John E Hallsworth / Alexandra A Klyukina / Ekaterina N Tikhonova / Vladimir M Gorlenko / Abstract: Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress ...Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress factor that is biotic: a diminutive Candidate-Phyla-Radiation bacterium, that we named 'Ca. Absconditicoccus praedator' M39-6, which predates H. halophila M39-5, an obligately photosynthetic, anaerobic purple-sulfur bacterium. We cultivated this association (isolated from the hypersaline alkaline Lake Hotontyn Nur, Mongolia) and characterized their biology. 'Ca. Absconditicoccus praedator' is the first stably cultivated species from the candidate class-level lineage Gracilibacteria (order-level lineage Absconditabacterales). Its closed-and-curated genome lacks genes for the glycolytic, pentose phosphate- and Entner-Doudoroff pathways which would generate energy/reducing equivalents and produce central carbon currencies. Therefore, 'Ca. Absconditicoccus praedator' is dependent on host-derived building blocks for nucleic acid-, protein-, and peptidoglycan synthesis. It shares traits with (the uncultured) 'Ca. Vampirococcus lugosii', which is also of the Gracilibacteria lineage. These are obligate parasitic lifestyle, feeding on photosynthetic anoxygenic Gammaproteobacteria, and absorption of host cytoplasm. Commonalities in their genomic composition and structure suggest that the entire Absconditabacterales lineage consists of predatory species which act to cull the populations of their respective host bacteria. Cultivation of vampire : host associations can shed light on unresolved aspects of their metabolism and ecosystem dynamics at life-limiting extremes. | |||||||||
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-Structure visualization
Movie |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13730.map.gz | 68.5 MB | EMDB map data format | |
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Header (meta data) | emd-13730-v30.xml emd-13730.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_13730.png | 246.4 KB | ||
Filedesc metadata | emd-13730.cif.gz | 3.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13730 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13730 | HTTPS FTP |
-Validation report
Summary document | emd_13730_validation.pdf.gz | 443 KB | Display | EMDB validaton report |
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Full document | emd_13730_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | emd_13730_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | emd_13730_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13730 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13730 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13730.map.gz / Format: CCP4 / Size: 167.6 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 18.28 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 : Cryo-electron tomography of an attached epibiotic cell of Ca. Abs...
Entire | Name: Cryo-electron tomography of an attached epibiotic cell of Ca. Absconditicoccus predator |
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Components |
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-Supramolecule #1: Cryo-electron tomography of an attached epibiotic cell of Ca. Abs...
Supramolecule | Name: Cryo-electron tomography of an attached epibiotic cell of Ca. Absconditicoccus predator type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: bacterium (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 9 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Details: PELCO easiGlowTM Ted Pella 15 mA for 15 s |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
Cryo protectant | no cryo-protectant |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Cytodiagnostics / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.4 sec. / Average electron dose: 2.524 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.11.5) / Number images used: 61 |
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