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- EMDB-23289: native AMPA receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-23289
Titlenative AMPA receptor
Map data
Sample
  • Complex: GluA1/A2/A3-asymmetric-conformation1 with bound antibody fragments
Function / homology
Function and homology information


Activation of AMPA receptors / Synaptic adhesion-like molecules / Cargo concentration in the ER / Unblocking of NMDA receptors, glutamate binding and activation / 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 ...Activation of AMPA receptors / Synaptic adhesion-like molecules / Cargo concentration in the ER / Unblocking of NMDA receptors, glutamate binding and activation / 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 / cellular response to ammonium ion / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / myosin V binding / neuron spine / response to arsenic-containing substance / cellular response to dsRNA / dendritic spine membrane / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / long-term synaptic depression / cellular response to peptide hormone stimulus / protein kinase A binding / spinal cord development / spine synapse / neuronal cell body membrane / dendritic spine neck / dendritic spine head / perisynaptic space / AMPA glutamate receptor activity / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / adenylate cyclase binding / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / excitatory synapse / asymmetric synapse / regulation of receptor recycling / G-protein alpha-subunit binding / neuronal action potential / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / long-term memory / response to electrical stimulus / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / beta-2 adrenergic receptor binding / response to fungicide / regulation of synaptic transmission, glutamatergic / 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 / cytoskeletal protein binding / dendrite cytoplasm / SNARE binding / 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 / long-term synaptic potentiation / protein tetramerization / cellular response to amino acid stimulus / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / regulation of synaptic plasticity / neuromuscular junction / terminal bouton / 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 / signaling receptor activity / amyloid-beta binding / early endosome membrane / cell body / growth cone / scaffold protein binding / postsynapse / chemical synaptic transmission / postsynaptic membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor 1 / Glutamate receptor 2 / Glutamate receptor 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsYu J / Rao P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS038631 United States
CitationJournal: 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
DepositionJan 14, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23289.png

Downloads & links

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Map

FileDownload / File: emd_23289.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.611 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.31497878 - 1.014373
Average (Standard dev.)-0.00012855208 (±0.033470098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 515.51996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6111.6111.611
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z515.520515.520515.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ330330330
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.3151.014-0.000

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Supplemental data

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Sample components

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Entire : GluA1/A2/A3-asymmetric-conformation1 with bound antibody fragments

EntireName: GluA1/A2/A3-asymmetric-conformation1 with bound antibody fragments
Components
  • Complex: GluA1/A2/A3-asymmetric-conformation1 with bound antibody fragments

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Supramolecule #1: GluA1/A2/A3-asymmetric-conformation1 with bound antibody fragments

SupramoleculeName: GluA1/A2/A3-asymmetric-conformation1 with bound antibody fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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