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Yorodumi- EMDB-33808: Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33808 | |||||||||
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Title | Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the topiramate-bound state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Voltage-gated calcium channel / CaV2.3 / Complex / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of muscle contraction / regulation of membrane repolarization during action potential / Presynaptic depolarization and calcium channel opening / positive regulation of high voltage-gated calcium channel activity / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during bundle of His cell action potential / L-type voltage-gated calcium channel complex / cardiac muscle cell action potential involved in contraction / high voltage-gated calcium channel activity ...positive regulation of muscle contraction / regulation of membrane repolarization during action potential / Presynaptic depolarization and calcium channel opening / positive regulation of high voltage-gated calcium channel activity / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during bundle of His cell action potential / L-type voltage-gated calcium channel complex / cardiac muscle cell action potential involved in contraction / high voltage-gated calcium channel activity / voltage-gated monoatomic cation channel activity / NCAM1 interactions / regulation of ventricular cardiac muscle cell membrane repolarization / calcium ion transport into cytosol / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / neuromuscular junction development / voltage-gated calcium channel complex / neuronal dense core vesicle / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / regulation of calcium ion transport / calcium ion import across plasma membrane / voltage-gated calcium channel activity / sarcoplasmic reticulum / Regulation of insulin secretion / calcium ion transmembrane transport / cellular response to amyloid-beta / calcium ion transport / chemical synaptic transmission / neuronal cell body / synapse / calcium ion binding / extracellular exosome / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Gao Y / Zhao Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structural insights into allosteric effects of antiepileptic drug topiramate on CaV2.3 channel. Authors: Gao Y / Zhao Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33808.map.gz | 118.1 MB | EMDB map data format | |
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Header (meta data) | emd-33808-v30.xml emd-33808.xml | 23.9 KB 23.9 KB | Display Display | EMDB header |
Images | emd_33808.png | 97.5 KB | ||
Filedesc metadata | emd-33808.cif.gz | 9 KB | ||
Others | emd_33808_half_map_1.map.gz emd_33808_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33808 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33808 | HTTPS FTP |
-Related structure data
Related structure data | 7yg5MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33808.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33808_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33808_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human R-type voltage-gated calcium channel CaV2.3-alpha2/delta1-b...
+Supramolecule #1: Human R-type voltage-gated calcium channel CaV2.3-alpha2/delta1-b...
+Macromolecule #1: Voltage-dependent R-type calcium channel subunit alpha-1E
+Macromolecule #2: Voltage-dependent L-type calcium channel subunit beta-1
+Macromolecule #3: Voltage-dependent calcium channel subunit alpha-2/delta-1
+Macromolecule #6: CHOLESTEROL HEMISUCCINATE
+Macromolecule #7: HEXADECANE
+Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #9: CALCIUM ION
+Macromolecule #10: [(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]diox...
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 273 K / Instrument: FEI VITROBOT MARK IV |
Details | This sample was obtained from the monodispersed peak fractions of the size-exclusion chromatography. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 135000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 2097 / Average exposure time: 6.7 sec. / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 787518 |
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Startup model | Type of model: INSILICO MODEL In silico model: The insilico model was generated using the ab-initio reconstruction in cryoSPARC. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) |
Final 3D classification | Number classes: 6 / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 68522 |