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Yorodumi- EMDB-17163: Structure of the Bacterial Voltage-Gated Sodium Channel NaChBac i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17163 | |||||||||
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Title | Structure of the Bacterial Voltage-Gated Sodium Channel NaChBac in Liposomes | |||||||||
Map data | NaChBac/liposome | |||||||||
Sample |
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Keywords | Voltage-gated Sodium ion Channel / MEMBRANE PROTEIN | |||||||||
Biological species | Halalkalibacterium halodurans C-125 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 16.3 Å | |||||||||
Authors | Chang S-YS / Kudryashev M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Sci Rep / Year: 2023 Title: Determining the structure of the bacterial voltage-gated sodium channel NaChBac embedded in liposomes by cryo electron tomography and subtomogram averaging. Authors: Shih-Ying Scott Chang / Patricia M Dijkman / Simon A Wiessing / Misha Kudryashev / Abstract: Voltage-gated sodium channels shape action potentials that propagate signals along cells. When the membrane potential reaches a certain threshold, the channels open and allow sodium ions to flow ...Voltage-gated sodium channels shape action potentials that propagate signals along cells. When the membrane potential reaches a certain threshold, the channels open and allow sodium ions to flow through the membrane depolarizing it, followed by the deactivation of the channels. Opening and closing of the channels is important for cellular signalling and regulates various physiological processes in muscles, heart and brain. Mechanistic insights into the voltage-gated channels are difficult to achieve as the proteins are typically extracted from membranes for structural analysis which results in the loss of the transmembrane potential that regulates their activity. Here, we report the structural analysis of a bacterial voltage-gated sodium channel, NaChBac, reconstituted in liposomes under an electrochemical gradient by cryo electron tomography and subtomogram averaging. We show that the small channel, most of the residues of which are embedded in the membrane, can be localized using a genetically fused GFP. GFP can aid the initial alignment to an average resulting in a correct structure, but does not help for the final refinement. At a moderate resolution of ˜16 Å the structure of NaChBac in an unrestricted membrane bilayer is 10% wider than the structure of the purified protein previously solved in nanodiscs, suggesting the potential movement of the peripheral voltage-sensing domains. Our study explores the limits of structural analysis of membrane proteins in membranes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17163.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-17163-v30.xml emd-17163.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17163_fsc.xml | 6 KB | Display | FSC data file |
Images | emd_17163.png | 57.3 KB | ||
Masks | emd_17163_msk_1.map | 8 MB | Mask map | |
Others | emd_17163_half_map_1.map.gz emd_17163_half_map_2.map.gz | 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17163 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17163 | HTTPS FTP |
-Validation report
Summary document | emd_17163_validation.pdf.gz | 806.6 KB | Display | EMDB validaton report |
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Full document | emd_17163_full_validation.pdf.gz | 806.2 KB | Display | |
Data in XML | emd_17163_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_17163_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17163 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17163 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17163.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | NaChBac/liposome | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.786 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17163_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_17163_half_map_1.map | ||||||||||||
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Annotation | half_map_1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_17163_half_map_2.map | ||||||||||||
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Annotation | half_map_2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Sodium Ion Channel NaChBac in Liposomes
Entire | Name: Sodium Ion Channel NaChBac in Liposomes |
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Components |
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-Supramolecule #1: Sodium Ion Channel NaChBac in Liposomes
Supramolecule | Name: Sodium Ion Channel NaChBac in Liposomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Halalkalibacterium halodurans C-125 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 4.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |