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Yorodumi- EMDB-19937: 6-channel super-structure of the Mechanosensitive Ion Channel of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19937 | |||||||||||||||
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Title | 6-channel super-structure of the Mechanosensitive Ion Channel of Small Conductance 2 from Nematocida displodere | |||||||||||||||
Map data | Six homo-heptameric channels, formed by Nematocida displodere Mechanosensitive ion channel of small conductance 2, form a higher oligomeric structure resembling a six-way cross joint. | |||||||||||||||
Sample |
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Keywords | Membrane protein / channel protein | |||||||||||||||
Biological species | Nematocida displodere (fungus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.3 Å | |||||||||||||||
Authors | Berg A / Barandun J / Berntsson RP-A | |||||||||||||||
Funding support | Sweden, European Union, 4 items
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Citation | Journal: PLoS One / Year: 2024 Title: Nematocida displodere mechanosensitive ion channel of small conductance 2 assembles into a unique 6-channel super-structure in vitro. Authors: Alexandra Berg / Ronnie P-A Berntsson / Jonas Barandun / Abstract: Mechanosensitive ion channels play an essential role in reacting to environmental signals and sustaining cell integrity by facilitating ion flux across membranes. For obligate intracellular pathogens ...Mechanosensitive ion channels play an essential role in reacting to environmental signals and sustaining cell integrity by facilitating ion flux across membranes. For obligate intracellular pathogens like microsporidia, adapting to changes in the host environment is crucial for survival and propagation. Despite representing a eukaryote of extreme genome reduction, microsporidia have expanded the gene family of mechanosensitive ion channels of small conductance (mscS) through repeated gene duplication and horizontal gene transfer. All microsporidian genomes characterized to date contain mscS genes of both eukaryotic and bacterial origin. Here, we investigated the cryo-electron microscopy structure of the bacterially derived mechanosensitive ion channel of small conductance 2 (MscS2) from Nematocida displodere, an intracellular pathogen of Caenorhabditis elegans. MscS2 is the most compact MscS-like channel known and assembles into a unique superstructure in vitro with six heptameric MscS2 channels. Individual MscS2 channels are oriented in a heterogeneous manner to one another, resembling an asymmetric, flexible six-way cross joint. Finally, we show that microsporidian MscS2 still forms a heptameric membrane channel, however the extreme compaction suggests a potential new function of this MscS-like protein. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19937.map.gz | 196.3 MB | EMDB map data format | |
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Header (meta data) | emd-19937-v30.xml emd-19937.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19937_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_19937.png | 130.6 KB | ||
Masks | emd_19937_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-19937.cif.gz | 4.5 KB | ||
Others | emd_19937_additional_1.map.gz emd_19937_half_map_1.map.gz emd_19937_half_map_2.map.gz | 199.3 MB 170.4 MB 170.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19937 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19937 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19937.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Six homo-heptameric channels, formed by Nematocida displodere Mechanosensitive ion channel of small conductance 2, form a higher oligomeric structure resembling a six-way cross joint. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19937_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_19937_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19937_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19937_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Six homo-heptameric mechanosensitive ion channel of small conduct...
Entire | Name: Six homo-heptameric mechanosensitive ion channel of small conductance 2 |
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Components |
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-Supramolecule #1: Six homo-heptameric mechanosensitive ion channel of small conduct...
Supramolecule | Name: Six homo-heptameric mechanosensitive ion channel of small conductance 2 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Nematocida displodere (fungus) |
Molecular weight | Theoretical: 64 KDa |
-Supramolecule #2: Homo-heptameric mechanosensitive ion channel of small conductance 2
Supramolecule | Name: Homo-heptameric mechanosensitive ion channel of small conductance 2 type: organelle_or_cellular_component / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Nematocida displodere (fungus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.288 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2000 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 190000 |
Sample stage | Cooling holder cryogen: NITROGEN |