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Yorodumi- EMDB-20487: Human alpha3beta4 nicotinic acetylcholine receptor in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20487 | |||||||||||||||||||||
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Title | Human alpha3beta4 nicotinic acetylcholine receptor in complex with nicotine | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information regulation of acetylcholine secretion, neurotransmission / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / positive regulation of transmission of nerve impulse / Highly calcium permeable nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex ...regulation of acetylcholine secretion, neurotransmission / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / positive regulation of transmission of nerve impulse / Highly calcium permeable nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / regulation of smooth muscle contraction / cholinergic synapse / regulation of neurotransmitter secretion / behavioral response to nicotine / acetylcholine-gated monoatomic cation-selective channel activity / synaptic transmission, cholinergic / neurotransmitter receptor activity / nervous system process / acetylcholine binding / acetylcholine receptor signaling pathway / activation of transmembrane receptor protein tyrosine kinase activity / regulation of dendrite morphogenesis / plasma membrane raft / membrane depolarization / tertiary granule membrane / ligand-gated monoatomic ion channel activity / neuronal action potential / smooth muscle contraction / specific granule membrane / monoatomic ion transport / excitatory postsynaptic potential / regulation of membrane potential / monoatomic ion transmembrane transport / locomotory behavior / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to nicotine / nervous system development / chemical synaptic transmission / postsynaptic membrane / postsynaptic density / electron transfer activity / periplasmic space / neuron projection / nuclear speck / iron ion binding / dendrite / neuronal cell body / synapse / heme binding / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / signal transduction / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) / house mouse (house mouse) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.34 Å | |||||||||||||||||||||
Authors | Gharpure A / Teng J / Zhuang Y / Noviello CM / Walsh RM / Cabuco R / Howard RJ / Zaveri NT / Lindahl E / Hibbs RE | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Neuron / Year: 2019 Title: Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic Receptor. Authors: Anant Gharpure / Jinfeng Teng / Yuxuan Zhuang / Colleen M Noviello / Richard M Walsh / Rico Cabuco / Rebecca J Howard / Nurulain T Zaveri / Erik Lindahl / Ryan E Hibbs / Abstract: Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The α3β4 nicotinic receptor subtype forms the principal relay between the central and ...Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The α3β4 nicotinic receptor subtype forms the principal relay between the central and peripheral nervous systems in the autonomic ganglia. This receptor is also expressed focally in brain areas that affect reward circuits and addiction. Here, we present structures of the α3β4 nicotinic receptor in lipidic and detergent environments, using functional reconstitution to define lipids appropriate for structural analysis. The structures of the receptor in complex with nicotine, as well as the α3β4-selective ligand AT-1001, complemented by molecular dynamics, suggest principles of agonist selectivity. The structures further reveal much of the architecture of the intracellular domain, where mutagenesis experiments and simulations define residues governing ion conductance. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20487.map.gz | 9.3 MB | EMDB map data format | |
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Header (meta data) | emd-20487-v30.xml emd-20487.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
Images | emd_20487.png | 31.4 KB | ||
Others | emd_20487_half_map_1.map.gz emd_20487_half_map_2.map.gz | 80.7 MB 80.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20487 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20487 | HTTPS FTP |
-Related structure data
Related structure data | 6pv7MC 6pv8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20487.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_20487_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_20487_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human alpha3beta4 nicotinic receptor in complex with Fab fragment...
+Supramolecule #1: Human alpha3beta4 nicotinic receptor in complex with Fab fragment...
+Supramolecule #2: Human alpha3beta4 nicotinic acetylcholine receptor
+Supramolecule #3: Neuronal acetylcholine receptor subunit alpha-3
+Supramolecule #4: Neuronal acetylcholine receptor subunit beta-4
+Supramolecule #5: IgG2b/kappa antibody
+Supramolecule #6: IgG2b heavy chain
+Supramolecule #7: Kappa Fab light chain
+Macromolecule #1: Fusion protein of Neuronal acetylcholine receptor subunit alpha-3...
+Macromolecule #2: Fusion protein of Neuronal acetylcholine receptor subunit beta-4 ...
+Macromolecule #3: IgG2b Fab heavy chain
+Macromolecule #4: Kappa Fab light chain
+Macromolecule #8: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
+Macromolecule #9: CHOLESTEROL HEMISUCCINATE
+Macromolecule #10: SODIUM ION
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #12: nonane
+Macromolecule #13: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 46730 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 / Number real images: 5053 / Average exposure time: 10.0 sec. / Average electron dose: 47.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 705401 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: OTHER / Details: De novo initial model from Relion |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 112737 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6pv7: |