[English] 日本語
Yorodumi- EMDB-28376: Structure of a human EMC:human Cav1.2 channel complex in GDN dete... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28376 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of a human EMC:human Cav1.2 channel complex in GDN detergent (ECAB Map 3) | |||||||||
Map data | Structure of a human EMC:human Cav1.2 channel complex in GDN detergent (ECAB Map 3) | |||||||||
Sample |
| |||||||||
Keywords | endoplasmic reticulum membrane protein complex / voltage-gated calcium channel / holdase / biogenesis / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / magnesium ion transport / cobalt ion transmembrane transporter activity ...extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / magnesium ion transport / cobalt ion transmembrane transporter activity / positive regulation of high voltage-gated calcium channel activity / membrane depolarization during atrial cardiac muscle cell action potential / tail-anchored membrane protein insertion into ER membrane / Phase 2 - plateau phase / Miscellaneous transport and binding events / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of muscle contraction / ferrous iron transmembrane transporter activity / magnesium ion transmembrane transporter activity / membrane depolarization during AV node cell action potential / positive regulation of adenylate cyclase activity / high voltage-gated calcium channel activity / copper ion transport / cardiac conduction / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / cell communication by electrical coupling involved in cardiac conduction / regulation of ventricular cardiac muscle cell action potential / alpha-actinin binding / cardiac muscle cell action potential involved in contraction / camera-type eye development / NCAM1 interactions / embryonic forelimb morphogenesis / calcium ion transport into cytosol / voltage-gated calcium channel complex / calcium ion import across plasma membrane / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / autophagosome assembly / calcium channel regulator activity / RHOA GTPase cycle / voltage-gated calcium channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / Regulation of insulin secretion / calcium ion transmembrane transport / postsynaptic density membrane / Z disc / Adrenaline,noradrenaline inhibits insulin secretion / positive regulation of angiogenesis / early endosome membrane / heart development / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / perikaryon / angiogenesis / calmodulin binding / postsynaptic density / early endosome / Golgi membrane / dendrite / endoplasmic reticulum membrane / apoptotic process / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Chen Z / Mondal A / Abderemane-Ali F / Minor DL | |||||||||
Funding support | United States, 2 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28376.map.gz | 260.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28376-v30.xml emd-28376.xml | 27.9 KB 27.9 KB | Display Display | EMDB header |
Images | emd_28376.png | 132 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28376 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28376 | HTTPS FTP |
-Validation report
Summary document | emd_28376_validation.pdf.gz | 507.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_28376_full_validation.pdf.gz | 507.1 KB | Display | |
Data in XML | emd_28376_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_28376_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28376 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28376 | HTTPS FTP |
-Related structure data
Related structure data | 8eoiMC 8eogC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_28376.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Structure of a human EMC:human Cav1.2 channel complex in GDN detergent (ECAB Map 3) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8466 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
+Entire : Ternary complex of the human ER membrane protein complex (EMC) wi...
+Supramolecule #1: Ternary complex of the human ER membrane protein complex (EMC) wi...
+Supramolecule #2: Human CaV alpha1C
+Supramolecule #3: ER membrane protein complex subunit 1
+Supramolecule #4: Rabbit CaV beta3
+Macromolecule #1: ER membrane protein complex subunit 1
+Macromolecule #2: ER membrane protein complex subunit 2
+Macromolecule #3: ER membrane protein complex subunit 3
+Macromolecule #4: ER membrane protein complex subunit 5
+Macromolecule #5: ER membrane protein complex subunit 6
+Macromolecule #6: ER membrane protein complex subunit 7
+Macromolecule #7: ER membrane protein complex subunit 8
+Macromolecule #8: ER membrane protein complex subunit 10
+Macromolecule #9: Voltage-dependent L-type calcium channel subunit alpha-1C
+Macromolecule #10: Voltage-dependent L-type calcium channel subunit beta-3
+Macromolecule #11: ER membrane protein complex subunit 4
+Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #14: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.7 mg/mL |
---|---|
Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / 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 |
---|---|
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: Details: 6WW7 (PDB ID) and 7MIY (PDB ID) used to generate the startup model. |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 487067 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |