+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23284 | |||||||||
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Title | native AMPA receptor | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Phase 2 - plateau phase / Activation of AMPA receptors / Phase 0 - rapid depolarisation / negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Synaptic adhesion-like molecules / Cargo concentration in the ER / Unblocking of NMDA receptors, glutamate binding and activation / LGI-ADAM interactions / COPII-mediated vesicle transport ...Phase 2 - plateau phase / Activation of AMPA receptors / Phase 0 - rapid depolarisation / negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Synaptic adhesion-like molecules / Cargo concentration in the ER / Unblocking of NMDA receptors, glutamate binding and activation / LGI-ADAM interactions / COPII-mediated vesicle transport / Trafficking of AMPA receptors / cellular response to amine stimulus / axonal spine / Trafficking of GluR2-containing AMPA receptors / positive regulation of membrane potential / localization within membrane / cellular response to ammonium ion / neurotransmitter receptor transport, postsynaptic endosome to lysosome / L-type voltage-gated calcium channel complex / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / myosin V binding / neuron spine / regulation of AMPA receptor activity / neurotransmitter receptor internalization / channel regulator activity / protein phosphatase 2B binding / response to arsenic-containing substance / cellular response to dsRNA / postsynaptic neurotransmitter receptor diffusion trapping / dendritic spine membrane / glutamate-gated calcium ion channel activity / anchoring junction / long-term synaptic depression / cellular response to peptide hormone stimulus / protein kinase A binding / spinal cord development / neuronal cell body membrane / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / COPII-coated ER to Golgi transport vesicle / regulation of postsynaptic membrane neurotransmitter receptor levels / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / adenylate cyclase binding / ionotropic glutamate receptor complex / excitatory synapse / calcium channel regulator activity / asymmetric synapse / regulation of receptor recycling / G-protein alpha-subunit binding / voltage-gated calcium channel activity / neuronal action potential / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / long-term memory / endoplasmic reticulum to Golgi vesicle-mediated transport / response to electrical stimulus / glutamate-gated receptor activity / presynaptic active zone membrane / beta-2 adrenergic receptor binding / response to fungicide / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / synapse assembly / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of synaptic transmission, glutamatergic / response to cocaine / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / regulation of membrane potential / long-term synaptic potentiation / cellular response to amino acid stimulus / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / regulation of synaptic plasticity / neuromuscular junction / receptor internalization / response to toxic substance / cerebral cortex development / synaptic vesicle membrane / small GTPase binding / recycling endosome membrane / G-protein beta-subunit binding / cell-cell junction / synaptic vesicle / presynapse / response to estradiol / presynaptic membrane / amyloid-beta binding / early endosome membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Mouse (mice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Yu J / Rao P / Gouaux E | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2021 Title: Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition. Authors: Jie Yu / Prashant Rao / Sarah Clark / Jaba Mitra / Taekjip Ha / Eric Gouaux / Abstract: AMPA-selective glutamate receptors mediate the transduction of signals between the neuronal circuits of the hippocampus. The trafficking, localization, kinetics and pharmacology of AMPA receptors are ...AMPA-selective glutamate receptors mediate the transduction of signals between the neuronal circuits of the hippocampus. The trafficking, localization, kinetics and pharmacology of AMPA receptors are tuned by an ensemble of auxiliary protein subunits, which are integral membrane proteins that associate with the receptor to yield bona fide receptor signalling complexes. Thus far, extensive studies of recombinant AMPA receptor-auxiliary subunit complexes using engineered protein constructs have not been able to faithfully elucidate the molecular architecture of hippocampal AMPA receptor complexes. Here we obtain mouse hippocampal, calcium-impermeable AMPA receptor complexes using immunoaffinity purification and use single-molecule fluorescence and cryo-electron microscopy experiments to elucidate three major AMPA receptor-auxiliary subunit complexes. The GluA1-GluA2, GluA1-GluA2-GluA3 and GluA2-GluA3 receptors are the predominant assemblies, with the auxiliary subunits TARP-γ8 and CNIH2-SynDIG4 non-stochastically positioned at the B'/D' and A'/C' positions, respectively. We further demonstrate how the receptor-TARP-γ8 stoichiometry explains the mechanism of and submaximal inhibition by a clinically relevant, brain-region-specific allosteric inhibitor. | |||||||||
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_23284.map.gz | 483.5 MB | EMDB map data format | |
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Header (meta data) | emd-23284-v30.xml emd-23284.xml | 26.6 KB 26.6 KB | Display Display | EMDB header |
Images | emd_23284.png | 113.6 KB | ||
Others | emd_23284_additional_1.map.gz emd_23284_additional_2.map.gz | 483.6 MB 245.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23284 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23284 | HTTPS FTP |
-Validation report
Summary document | emd_23284_validation.pdf.gz | 445.2 KB | Display | EMDB validaton report |
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Full document | emd_23284_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | emd_23284_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_23284_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23284 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23284 | HTTPS FTP |
-Related structure data
Related structure data | 7ldeMC 7lddC 7lepC 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_23284.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.00687 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #2
File | emd_23284_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_23284_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : GluA1/A2-asymmetric-conformation bound to antibody fragments
+Supramolecule #1: GluA1/A2-asymmetric-conformation bound to antibody fragments
+Supramolecule #2: GluA1/A2-asymmetric-conformation
+Supramolecule #3: 11B8 scFv
+Supramolecule #4: 15F1 Fab
+Macromolecule #1: Glutamate receptor 1
+Macromolecule #2: Glutamate receptor
+Macromolecule #3: Protein cornichon homolog 2
+Macromolecule #4: Voltage-dependent calcium channel gamma-8 subunit
+Macromolecule #5: 11B8 scFv
+Macromolecule #6: 15F1 Fab light chain
+Macromolecule #7: 15F1 Fab heavy chain
+Macromolecule #9: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquino...
+Macromolecule #10: HEXADECANE
+Macromolecule #11: N-OCTANE
+Macromolecule #12: HEPTANE
+Macromolecule #13: DECANE
+Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #15: DODECANE
+Macromolecule #16: TETRADECANE
+Macromolecule #17: nonane
+Macromolecule #18: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157000 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |