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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9388 | |||||||||
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Title | Architecture and subunit arrangement of native AMPA receptors | |||||||||
![]() | Structure of a complex | |||||||||
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Function / homology | ![]() Presynaptic depolarization and calcium channel opening / chemical synaptic transmission, postsynaptic / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / LGI-ADAM interactions / Trafficking of AMPA receptors / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Gouaux E / Zhao Y | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 30.6 KB 30.6 KB | Display Display | ![]() |
Images | ![]() | 126.5 KB | ||
Others | ![]() ![]() ![]() | 8.4 MB 8 MB 7.4 MB | ||
Archive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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_9388_additional_1.map | ||||||||||||
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Annotation | Structure of a complex | ||||||||||||
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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 | ||||||||||||
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-Additional map: Structure of a complex
File | emd_9388_additional_3.map | ||||||||||||
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Annotation | Structure of a complex | ||||||||||||
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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 | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 54.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Initial angle assignment | Type: RANDOM ASSIGNMENT |
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Final 3D classification | Number classes: 10 |
Final angle assignment | Type: RANDOM ASSIGNMENT |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 99000 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-6njm: |