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Yorodumi- PDB-7uhf: Human L-type voltage-gated calcium channel Cav1.3 in the presence... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uhf | ||||||
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Title | Human L-type voltage-gated calcium channel Cav1.3 in the presence of cinnarizine at 3.1 Angstrom resolution | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Cav1.3 / Channels / Calcium Ion-Selective | ||||||
Function / homology | Function and homology information voltage-gated calcium channel activity involved SA node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / membrane depolarization during SA node cell action potential / regulation of membrane repolarization during action potential / Presynaptic depolarization and calcium channel opening / regulation of potassium ion transmembrane transporter activity / positive regulation of high voltage-gated calcium channel activity / regulation of atrial cardiac muscle cell membrane repolarization / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during bundle of His cell action potential ...voltage-gated calcium channel activity involved SA node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / membrane depolarization during SA node cell action potential / regulation of membrane repolarization during action potential / Presynaptic depolarization and calcium channel opening / regulation of potassium ion transmembrane transporter activity / positive regulation of high voltage-gated calcium channel activity / regulation of atrial cardiac muscle cell membrane repolarization / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during bundle of His cell action potential / positive regulation of adenylate cyclase activity / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / high voltage-gated calcium channel activity / positive regulation of calcium ion transport / regulation of potassium ion transmembrane transport / NCAM1 interactions / regulation of ventricular cardiac muscle cell membrane repolarization / calcium ion import / Sensory processing of sound by inner hair cells of the cochlea / calcium ion transport into cytosol / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / ankyrin binding / neuromuscular junction development / voltage-gated calcium channel complex / neuronal dense core vesicle / regulation of heart rate by cardiac conduction / alpha-actinin binding / calcium ion import across plasma membrane / calcium channel regulator activity / regulation of calcium ion transport / voltage-gated calcium channel activity / sarcoplasmic reticulum / Regulation of insulin secretion / protein localization to plasma membrane / calcium ion transmembrane transport / sensory perception of sound / calcium channel activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Adrenaline,noradrenaline inhibits insulin secretion / Z disc / cellular response to amyloid-beta / calcium ion transport / T cell receptor signaling pathway / chemical synaptic transmission / synapse / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Gao, S. / Yao, X. / Yan, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Res / Year: 2022 Title: Structural basis for pore blockade of human voltage-gated calcium channel Ca1.3 by motion sickness drug cinnarizine. Authors: Xia Yao / Shuai Gao / Nieng Yan / | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uhf.cif.gz | 477.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uhf.ent.gz | 375.7 KB | Display | PDB format |
PDBx/mmJSON format | 7uhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/7uhf ftp://data.pdbj.org/pub/pdb/validation_reports/uh/7uhf | HTTPS FTP |
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-Related structure data
Related structure data | 26513MC 7uhgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Voltage-dependent L-type calcium channel subunit ... , 2 types, 2 molecules AC
#1: Protein | Mass: 245417.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CACNA1D, CACH3, CACN4, CACNL1A2, CCHL1A2 / Production host: Homo sapiens (human) / References: UniProt: Q01668 |
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#3: Protein | Mass: 54607.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CACNB3, CACNLB3 / Production host: Homo sapiens (human) / References: UniProt: P54284 |
-Protein , 1 types, 1 molecules D
#2: Protein | Mass: 124692.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CACNA2D1, CACNL2A, CCHL2A, MHS3 / Production host: Homo sapiens (human) / References: UniProt: P54289 |
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-Sugars , 4 types, 8 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | |
-Non-polymers , 4 types, 5 molecules
#7: Chemical | ChemComp-N90 / | ||||
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#9: Chemical | #10: Chemical | ChemComp-Y01 / | #11: Chemical | ChemComp-3PE / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cav1.3 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2100 nm / Nominal defocus min: 1900 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51625 / Symmetry type: POINT | ||||||||||||||||||||||||
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