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- EMDB-2363: Electron tomogram through a Gemmata obscuriglobus cell -

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Basic information

Entry
Database: EMDB / ID: EMD-2363
TitleElectron tomogram through a Gemmata obscuriglobus cell
Map dataTomographic reconstruction through a whole gemmata obscuriglobus cell.
Sample
  • Sample: Gemmata obscuriglobus cell
  • Organelle or cellular component: Gemmata obscuriglobus
Keywordsendomembrane / eukaryogenesis / electron tomography
Biological speciesGemmata obscuriglobus (bacteria)
Methodelectron tomography / cryo EM / negative staining
AuthorsSantarella-Mellwig R / Pruggnaller S / Roos N / Mattaj IW / Devos DP
CitationJournal: PLoS Biol / Year: 2013
Title: Three-dimensional reconstruction of bacteria with a complex endomembrane system.
Authors: Rachel Santarella-Mellwig / Sabine Pruggnaller / Norbert Roos / Iain W Mattaj / Damien P Devos /
Abstract: The division of cellular space into functionally distinct membrane-defined compartments has been one of the major transitions in the history of life. Such compartmentalization has been claimed to ...The division of cellular space into functionally distinct membrane-defined compartments has been one of the major transitions in the history of life. Such compartmentalization has been claimed to occur in members of the Planctomycetes, Verrucomicrobiae, and Chlamydiae bacterial superphylum. Here we have investigated the three-dimensional organization of the complex endomembrane system in the planctomycete bacteria Gemmata obscuriglobus. We reveal that the G. obscuriglobus cells are neither compartmentalized nor nucleated as none of the spaces created by the membrane invaginations are closed; instead, they are all interconnected. Thus, the membrane organization of G. obscuriglobus, and most likely all PVC members, is not different from, but an extension of, the "classical" Gram-negative bacterial membrane system. Our results have implications for our definition and understanding of bacterial cell organization, the genesis of complex structure, and the origin of the eukaryotic endomembrane system.
History
DepositionApr 16, 2013-
Header (metadata) releaseMay 1, 2013-
Map releaseJun 5, 2013-
UpdateAug 21, 2013-
Current statusAug 21, 2013Processing 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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  • Simplified surface model
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2363-Gem...

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Map

FileDownload / File: emd_2363.map.gz / Format: CCP4 / Size: 2.9 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomographic reconstruction through a whole gemmata obscuriglobus cell.
Voxel sizeX=Y=Z: 15 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)39.31257248 (±33.533790590000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions165916531161
Spacing165916531161
CellA: 24795.0 Å / B: 24885.0 Å / C: 17415.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z151515
M x/y/z165316591161
origin x/y/z0.0000.0000.000
length x/y/z24795.00024885.00017415.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS165316591161
D min/max/mean-128.000127.00039.313

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Supplemental data

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Sample components

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Entire : Gemmata obscuriglobus cell

EntireName: Gemmata obscuriglobus cell
Components
  • Sample: Gemmata obscuriglobus cell
  • Organelle or cellular component: Gemmata obscuriglobus

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Supramolecule #1000: Gemmata obscuriglobus cell

SupramoleculeName: Gemmata obscuriglobus cell / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Gemmata obscuriglobus

SupramoleculeName: Gemmata obscuriglobus / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gemmata obscuriglobus (bacteria) / Strain: DSM-5831

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

StainingType: NEGATIVE
Details: High pressure frozen/freeze substituted in 0.5% uranyl acetate
VitrificationCryogen name: NITROGEN / Instrument: OTHER
Method: high pressure frozen with 100 micrometer deep carriers

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 15500
Sample stageSpecimen holder model: OTHER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 1 °
DateJun 30, 2010
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 120

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