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- EMDB-23290: native AMPA receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-23290
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 / COPII-mediated vesicle transport / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to amine stimulus / axonal spine / Trafficking of GluR2-containing AMPA receptors / Trafficking of AMPA receptors / positive regulation of membrane potential ...Activation of AMPA receptors / Synaptic adhesion-like molecules / Cargo concentration in the ER / COPII-mediated vesicle transport / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to amine stimulus / axonal spine / Trafficking of GluR2-containing AMPA receptors / Trafficking of AMPA receptors / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior / cellular response to ammonium ion / response to sucrose / proximal dendrite / myosin V binding / neuron spine / cellular response to L-glutamate / regulation of monoatomic ion transmembrane transport / conditioned place preference / response to arsenic-containing substance / cellular response to dsRNA / dendritic spine membrane / long-term synaptic depression / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / response to morphine / neuronal cell body membrane / peptide hormone receptor binding / protein kinase A binding / protein heterotetramerization / response to psychosocial stress / spinal cord development / parallel fiber to Purkinje cell synapse / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / response to lithium ion / immunoglobulin binding / behavioral response to pain / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / adenylate cyclase binding / excitatory synapse / positive regulation of excitatory postsynaptic potential / regulation of receptor recycling / G-protein alpha-subunit binding / long-term memory / postsynaptic density, intracellular component / glutamate receptor binding / neuronal action potential / response to electrical stimulus / glutamate-gated receptor activity / synapse assembly / response to fungicide / presynaptic active zone membrane / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / response to cocaine / synaptic membrane / response to nutrient levels / postsynaptic density membrane / neuromuscular junction / Schaffer collateral - CA1 synapse / cerebral cortex development / small GTPase binding / receptor internalization / long-term synaptic potentiation / synaptic vesicle membrane / recycling endosome membrane / synaptic vesicle / G-protein beta-subunit binding / cell-cell junction / response to estradiol / presynapse / amyloid-beta binding / cell body / early endosome membrane / scaffold protein binding / chemical synaptic transmission / protein homotetramerization / dendritic spine / response to ethanol / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / response to xenobiotic stimulus / external side of plasma membrane / neuronal cell body / synapse / dendrite / positive regulation of gene expression
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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: 7.5 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: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23290.png

Downloads & links

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Map

FileDownload / File: emd_23290.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 320 pix.
= 515.52 Å		1.61 Å/pix.
x 320 pix.
= 515.52 Å		1.61 Å/pix.
x 320 pix.
= 515.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.611 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.28883582 - 0.95460784
Average (Standard dev.)3.9346447e-05 (±0.035104644)
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-0.2890.9550.000

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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: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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