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Yorodumi- EMDB-16061: Electron cryotomogram of septal region from FIB milled filament o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16061 | ||||||||||||
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Title | Electron cryotomogram of septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN-mbp-sfgfp mutant | ||||||||||||
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Sample |
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Keywords | Cell-cell communication / Septal junctions / Filamentous cyanobacteria / Nostoc PCC 7120 / STRUCTURAL PROTEIN | ||||||||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Kieninger A / Tokarz P / Janovic A / Pilhofer M / Weiss G / Maldener I | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: SepN is a septal junction component required for gated cell-cell communication in the filamentous cyanobacterium Nostoc. Authors: Ann-Katrin Kieninger / Piotr Tokarz / Ana Janović / Martin Pilhofer / Gregor L Weiss / Iris Maldener / Abstract: Multicellular organisms require controlled intercellular communication for their survival. Strains of the filamentous cyanobacterium Nostoc regulate cell-cell communication between sister cells via a ...Multicellular organisms require controlled intercellular communication for their survival. Strains of the filamentous cyanobacterium Nostoc regulate cell-cell communication between sister cells via a conformational change in septal junctions. These multi-protein cell junctions consist of a septum spanning tube with a membrane-embedded plug at both ends, and a cap covering the plug on the cytoplasmic side. The identities of septal junction components are unknown, with exception of the protein FraD. Here, we identify and characterize a FraD-interacting protein, SepN, as the second component of septal junctions in Nostoc. We use cryo-electron tomography of cryo-focused ion beam-thinned cyanobacterial filaments to show that septal junctions in a sepN mutant lack a plug module and display an aberrant cap. The sepN mutant exhibits highly reduced cell-cell communication rates, as shown by fluorescence recovery after photobleaching experiments. Furthermore, the mutant is unable to gate molecule exchange through septal junctions and displays reduced filament survival after stress. Our data demonstrate the importance of controlling molecular diffusion between cells to ensure the survival of a multicellular organism. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16061.map.gz | 323.5 MB | EMDB map data format | |
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Header (meta data) | emd-16061-v30.xml emd-16061.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_16061.png | 216.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16061 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16061 | HTTPS FTP |
-Validation report
Summary document | emd_16061_validation.pdf.gz | 411.8 KB | Display | EMDB validaton report |
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Full document | emd_16061_full_validation.pdf.gz | 411.4 KB | Display | |
Data in XML | emd_16061_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_16061_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16061 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16061 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16061.map.gz / Format: CCP4 / Size: 348.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 13.52 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : The septal region from FIB milled filament of Nostoc sp. PCC 7120...
Entire | Name: The septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN-mbp-sfgfp mutant |
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Components |
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-Supramolecule #1: The septal region from FIB milled filament of Nostoc sp. PCC 7120...
Supramolecule | Name: The septal region from FIB milled filament of Nostoc sp. PCC 7120 sepN-mbp-sfgfp mutant type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Details: BG11 broth |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV |
Details | Thin lamellae through plunge-frozen Nostoc filaments |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 3 / Focused ion beam - Current: 0.058 / Focused ion beam - Duration: 1500 / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 3000 / Focused ion beam - Final thickness: 200 Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam 550. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: Dynamo / Number images used: 41 |
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