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- EMDB-10806: Chloroflexus aggregans end cell -

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Basic information

Entry
Database: EMDB / ID: EMD-10806
TitleChloroflexus aggregans end cell
Map dataChloroflexus aggregans end cell. Segmentation of the cell is available on Fig 4.
Sample
  • Cell: Viridilinea mediisalina
Biological speciesCandidatus Viridilinea mediisalina (bacteria)
Methodelectron tomography / cryo EM
AuthorsGaisin VA / Kooger R / Pilhofer M
Funding supportEuropean Union, Russian Federation, 2 items
OrganizationGrant numberCountry
Russian Science FoundationFEMS-GO-2017-021European Union
Russian Foundation for Basic Research19-04-00423 Russian Federation
CitationJournal: Front Microbiol / Year: 2020
Title: Cryo-Electron Tomography Reveals the Complex Ultrastructural Organization of Multicellular Filamentous () Bacteria.
Authors: Vasil A Gaisin / Romain Kooger / Denis S Grouzdev / Vladimir M Gorlenko / Martin Pilhofer /
Abstract: The cell biology of is poorly studied. We applied cryo-focused ion beam milling and cryo-electron tomography to study the ultrastructural organization of thermophilic and , and mesophilic ". ...The cell biology of is poorly studied. We applied cryo-focused ion beam milling and cryo-electron tomography to study the ultrastructural organization of thermophilic and , and mesophilic ". Viridilinea mediisalina." These species represent the three main lineages within a group of multicellular filamentous anoxygenic phototrophic bacteria belonging to the order. We found surprising structural complexity in the . As with filamentous cyanobacteria, cells of and ". Viridilinea mediisalina" share the outer membrane-like layers of their intricate multilayer cell envelope. Additionally, cells of and ". Viridilinea mediisalina" are connected by septal channels that resemble cyanobacterial septal junctions. All three strains possess long pili anchored close to cell-to-cell junctions, a morphological feature comparable to that observed in cyanobacteria. The cytoplasm of the bacteria is crowded with intracellular organelles such as different types of storage granules, membrane vesicles, chlorosomes, gas vesicles, chemoreceptor-like arrays, and cytoplasmic filaments. We observed a higher level of complexity in the mesophilic strain compared to the thermophilic strains with regards to the composition of intracellular bodies and the organization of the cell envelope. The ultrastructural details that we describe in these bacteria will motivate further cell biological studies, given that the function and evolution of the many discovered morphological traits remain enigmatic in this diverse and widespread bacterial group.
History
DepositionMar 29, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseApr 8, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing 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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Movie viewer
Supplemental images

emd_10806.png

Downloads & links

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Map

FileDownload / File: emd_10806.map.gz / Format: CCP4 / Size: 339.8 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationChloroflexus aggregans end cell. Segmentation of the cell is available on Fig 4.
Voxel sizeX=Y=Z: 17.36 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)4.7886925 (±27.427963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928960400
Spacing960928400
CellA: 16665.602 Å / B: 16110.08 Å / C: 6944.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z17.36000208333317.3617.36
M x/y/z960928400
origin x/y/z0.0000.0000.000
length x/y/z16665.60216110.0806944.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS960928400
D min/max/mean-128.000127.0004.789

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Supplemental data

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Sample components

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Entire : Viridilinea mediisalina

EntireName: Viridilinea mediisalina
Components
  • Cell: Viridilinea mediisalina

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Supramolecule #1: Viridilinea mediisalina

SupramoleculeName: Viridilinea mediisalina / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Candidatus Viridilinea mediisalina (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 5.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 5 kV / Focused ion beam - Current: 0.035 nA / Focused ion beam - Duration: 300 sec. / Focused ion beam - Temperature: 125 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 300 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Helios. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file.

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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: 120.0 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 reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 61

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