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Yorodumi- EMDB-28564: Human L-type voltage-gated calcium channel Cav1.2 complexed with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28564 | |||||||||
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Title | Human L-type voltage-gated calcium channel Cav1.2 complexed with L-leucine (Segment Map 02) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | voltage-gated calcium channel / CaV alpha2delta / drug binding / gabapentinoid / MEMBRANE PROTEIN | |||||||||
Biological species | Homo sapiens (human) / Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Chen Z / Mondal A / Abderemane-Ali F / Minor DL | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2023 Title: EMC chaperone-Ca structure reveals an ion channel assembly intermediate. Authors: Zhou Chen / Abhisek Mondal / Fayal Abderemane-Ali / Seil Jang / Sangeeta Niranjan / José L Montaño / Balyn W Zaro / Daniel L Minor / Abstract: Voltage-gated ion channels (VGICs) comprise multiple structural units, the assembly of which is required for function. Structural understanding of how VGIC subunits assemble and whether chaperone ...Voltage-gated ion channels (VGICs) comprise multiple structural units, the assembly of which is required for function. Structural understanding of how VGIC subunits assemble and whether chaperone proteins are required is lacking. High-voltage-activated calcium channels (Cas) are paradigmatic multisubunit VGICs whose function and trafficking are powerfully shaped by interactions between pore-forming Ca1 or Ca2 Caα (ref. ), and the auxiliary Caβ and Caαδ subunits. Here we present cryo-electron microscopy structures of human brain and cardiac Ca1.2 bound with Caβ to a chaperone-the endoplasmic reticulum membrane protein complex (EMC)-and of the assembled Ca1.2-Caβ-Caαδ-1 channel. These structures provide a view of an EMC-client complex and define EMC sites-the transmembrane (TM) and cytoplasmic (Cyto) docks; interaction between these sites and the client channel causes partial extraction of a pore subunit and splays open the Caαδ-interaction site. The structures identify the Caαδ-binding site for gabapentinoid anti-pain and anti-anxiety drugs, show that EMC and Caαδ interactions with the channel are mutually exclusive, and indicate that EMC-to-Caαδ hand-off involves a divalent ion-dependent step and Ca1.2 element ordering. Disruption of the EMC-Ca complex compromises Ca function, suggesting that the EMC functions as a channel holdase that facilitates channel assembly. Together, the structures reveal a Ca assembly intermediate and EMC client-binding sites that could have wide-ranging implications for the biogenesis of VGICs and other membrane proteins. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28564.map.gz | 243.6 MB | EMDB map data format | |
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Header (meta data) | emd-28564-v30.xml emd-28564.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
Images | emd_28564.png | 41 KB | ||
Others | emd_28564_half_map_1.map.gz emd_28564_half_map_2.map.gz | 246.4 MB 246.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28564 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28564 | HTTPS FTP |
-Validation report
Summary document | emd_28564_validation.pdf.gz | 797.8 KB | Display | EMDB validaton report |
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Full document | emd_28564_full_validation.pdf.gz | 797.3 KB | Display | |
Data in XML | emd_28564_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | emd_28564_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28564 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28564 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28564.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8466 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28564_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28564_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of human CaV alpha1C and rabbit CaV beta3
Entire | Name: Ternary complex of human CaV alpha1C and rabbit CaV beta3 |
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Components |
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-Supramolecule #1: Ternary complex of human CaV alpha1C and rabbit CaV beta3
Supramolecule | Name: Ternary complex of human CaV alpha1C and rabbit CaV beta3 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Human CaV alpha1C
Supramolecule | Name: Human CaV alpha1C / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 187 KDa |
-Supramolecule #3: Rabbit CaV beta3
Supramolecule | Name: Rabbit CaV beta3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 100 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.7 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269802 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |