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Yorodumi- EMDB-23292: The composite LBD-TMD structure combined from all hippocampal AMP... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23292 | |||||||||
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Title | The composite LBD-TMD structure combined from all hippocampal AMPAR subtypes at 3.25 Angstrom resolution | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Phase 2 - plateau phase / Phase 0 - rapid depolarisation / negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Cargo concentration in the ER / COPII-mediated vesicle transport / LGI-ADAM interactions / Trafficking of AMPA receptors / localization within membrane / neurotransmitter receptor transport, postsynaptic endosome to lysosome ...Phase 2 - plateau phase / Phase 0 - rapid depolarisation / negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Cargo concentration in the ER / COPII-mediated vesicle transport / LGI-ADAM interactions / Trafficking of AMPA receptors / localization within membrane / neurotransmitter receptor transport, postsynaptic endosome to lysosome / L-type voltage-gated calcium channel complex / regulation of AMPA receptor activity / protein phosphatase 2B binding / neurotransmitter receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / transmission of nerve impulse / channel regulator activity / regulation of postsynaptic membrane neurotransmitter receptor levels / AMPA glutamate receptor complex / calcium channel regulator activity / voltage-gated calcium channel activity / positive regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / vesicle-mediated transport / dendrite membrane / ionotropic glutamate receptor binding / regulation of membrane potential / dendritic shaft / synaptic transmission, glutamatergic / postsynaptic density membrane / Schaffer collateral - CA1 synapse / postsynaptic membrane / membrane => GO:0016020 / dendritic spine / postsynaptic density / glutamatergic synapse / synapse / dendrite / endoplasmic reticulum membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Mouse (mice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 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_23292.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-23292-v30.xml emd-23292.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
Images | emd_23292.png | 132.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23292 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23292 | HTTPS FTP |
-Related structure data
Related structure data | 7lepMC 7lddC 7ldeC 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_23292.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1035 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Composite LBD-TMD complex from the combined hippocampal AMPAR subtypes
+Supramolecule #1: Composite LBD-TMD complex from the combined hippocampal AMPAR subtypes
+Macromolecule #1: Mix of AMPAR subunits (GluA1, GluA3, and GluA4)
+Macromolecule #2: Glutamate receptor 2
+Macromolecule #3: Mix of AMPAR subunits (GluA1, GluA3, and GluAX)
+Macromolecule #4: Protein cornichon homolog 2
+Macromolecule #5: Voltage-dependent calcium channel gamma-8 subunit
+Macromolecule #6: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquino...
+Macromolecule #7: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
+Macromolecule #8: TETRADECANE
+Macromolecule #9: DECANE
+Macromolecule #10: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
+Macromolecule #11: N-OCTANE
+Macromolecule #12: DODECANE
-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 / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (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 |