+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9387 | |||||||||
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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 / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion ...Presynaptic depolarization and calcium channel opening / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion / cerebellar mossy fiber / proximal dendrite / neurotransmitter receptor transport, postsynaptic endosome to lysosome / response to sucrose / LGI-ADAM interactions / myosin V binding / Trafficking of AMPA receptors / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / neuron spine / cellular response to L-glutamate / regulation of AMPA receptor activity / conditioned place preference / neurotransmitter receptor internalization / response to arsenic-containing substance / membrane hyperpolarization / postsynaptic neurotransmitter receptor diffusion trapping / cellular response to dsRNA / nervous system process / dendritic spine membrane / Synaptic adhesion-like molecules / protein targeting to membrane / regulation of monoatomic ion transmembrane transport / long-term synaptic depression / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / response to morphine / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / protein kinase A binding / peptide hormone receptor binding / neuromuscular junction development / response to psychosocial stress / spine synapse / dendritic spine neck / spinal cord development / dendritic spine head / neuronal cell body membrane / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / transmission of nerve impulse / ligand-gated monoatomic cation channel activity / channel regulator activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / regulation of postsynaptic membrane neurotransmitter receptor levels / behavioral response to pain / membrane depolarization / AMPA glutamate receptor complex / adenylate cyclase binding / kainate selective glutamate receptor activity / cellular response to organic cyclic compound / ionotropic glutamate receptor complex / positive regulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / cellular response to glycine / excitatory synapse / calcium channel regulator activity / neuronal action potential / asymmetric synapse / G-protein alpha-subunit binding / regulation of receptor recycling / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / voltage-gated calcium channel activity / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / long-term memory / extracellular ligand-gated monoatomic ion channel activity / response to electrical stimulus / glutamate-gated receptor activity / response to fungicide / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / SNARE binding Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Rat (rat) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 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_9387.map.gz | 10.7 MB | EMDB map data format | |
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Header (meta data) | emd-9387-v30.xml emd-9387.xml | 25.6 KB 25.6 KB | Display Display | EMDB header |
Images | emd_9387.png | 91.5 KB | ||
Others | emd_9387_additional_1.map.gz emd_9387_additional_2.map.gz emd_9387_additional_3.map.gz | 7.8 MB 8.9 MB 8.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9387 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9387 | HTTPS FTP |
-Validation report
Summary document | emd_9387_validation.pdf.gz | 314.6 KB | Display | EMDB validaton report |
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Full document | emd_9387_full_validation.pdf.gz | 314.1 KB | Display | |
Data in XML | emd_9387_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_9387_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9387 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9387 | HTTPS FTP |
-Related structure data
Related structure data | 6njlMC 0426C 0427C 0428C 0429C 0430C 0431C 0432C 9388C 9389C 6njmC 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_9387.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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_9387_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_9387_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_9387_additional_3.map | ||||||||||||
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Annotation | Structure of a complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Native A1A2A1A2 complex bound with MPQX
+Supramolecule #1: Native A1A2A1A2 complex bound with MPQX
+Macromolecule #1: Glutamate receptor 1
+Macromolecule #2: Glutamate receptor 2
+Macromolecule #3: A'/C' auxiliary proteins
+Macromolecule #4: Voltage-dependent calcium channel gamma-2 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: 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: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 130000 |
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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-6njl: |