+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9388 | |||||||||
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Title | Architecture and subunit arrangement of native AMPA receptors | |||||||||
Map data | Structure of a complex | |||||||||
Sample |
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Function / homology | Function and homology information Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / chemical synaptic transmission, postsynaptic / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / LGI-ADAM interactions / Trafficking of AMPA receptors / regulation of AMPA receptor activity / neurotransmitter receptor internalization ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / chemical synaptic transmission, postsynaptic / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / LGI-ADAM interactions / Trafficking of AMPA receptors / regulation of AMPA receptor activity / neurotransmitter receptor internalization / membrane hyperpolarization / postsynaptic neurotransmitter receptor diffusion trapping / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / parallel fiber to Purkinje cell synapse / voltage-gated calcium channel complex / protein heterotetramerization / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / channel regulator activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / regulation of postsynaptic membrane neurotransmitter receptor levels / immunoglobulin binding / membrane depolarization / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / calcium channel regulator activity / asymmetric synapse / regulation of receptor recycling / voltage-gated calcium channel activity / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / positive regulation of synaptic transmission, glutamatergic / synaptic cleft / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / response to fungicide / monoatomic ion transmembrane transport / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / long-term synaptic potentiation / protein tetramerization / postsynaptic density membrane / response to calcium ion / modulation of chemical synaptic transmission / establishment of protein localization / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / protein homotetramerization / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Rat (rat) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Gouaux E / Zhao Y | |||||||||
Citation | Journal: Science / Year: 2019 Title: Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM. Authors: Yan Zhao / Shanshuang Chen / Adam C Swensen / Wei-Jun Qian / Eric Gouaux / Abstract: Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric ...Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo-electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating. | |||||||||
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_9388.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-9388-v30.xml emd-9388.xml | 30.6 KB 30.6 KB | Display Display | EMDB header |
Images | emd_9388.png | 126.5 KB | ||
Others | emd_9388_additional_1.map.gz emd_9388_additional_2.map.gz emd_9388_additional_3.map.gz | 8.4 MB 8 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9388 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9388 | HTTPS FTP |
-Validation report
Summary document | emd_9388_validation.pdf.gz | 313.4 KB | Display | EMDB validaton report |
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Full document | emd_9388_full_validation.pdf.gz | 312.9 KB | Display | |
Data in XML | emd_9388_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_9388_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9388 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9388 | HTTPS FTP |
-Related structure data
Related structure data | 6njmMC 0426C 0427C 0428C 0429C 0430C 0431C 0432C 9387C 9389C 6njlC 6njnC 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_9388.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of a complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.72 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Structure of a complex
File | emd_9388_additional_1.map | ||||||||||||
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Annotation | Structure of a complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Structure of a complex
File | emd_9388_additional_2.map | ||||||||||||
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Annotation | Structure of a complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Structure of a complex
File | emd_9388_additional_3.map | ||||||||||||
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Annotation | Structure of a complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Native A3A2A3A2 complex bound with MPQX
+Supramolecule #1: Native A3A2A3A2 complex bound with MPQX
+Supramolecule #2: LBD-TMD layers of native A3A2A3A2 nAMPAR complex
+Supramolecule #3: ATD-LBD layers of native A3A2A3A2 nAMPAR complex
+Macromolecule #1: Glutamate receptor 3
+Macromolecule #2: Glutamate receptor 2
+Macromolecule #3: A'-C' auxiliary proteins
+Macromolecule #4: Voltage-dependent calcium channel gamma-2 subunit
+Macromolecule #5: 5B2 Fab Light Chain
+Macromolecule #6: 5B2 Fab Heavy Chain
+Macromolecule #7: 15F1 Fab light chain
+Macromolecule #8: 15F1 Fab heavy chain
+Macromolecule #11: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquino...
+Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Details: unspecified | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 54.0 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: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 99000 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |
Final 3D classification | Number classes: 10 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6njm: |