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- EMDB-48559: Desensitized state 2 of the GluA2-gamma2 complex prepared at 37 d... -

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Basic information

Entry
Database: EMDB / ID: EMD-48559
TitleDesensitized state 2 of the GluA2-gamma2 complex prepared at 37 degrees C
Map dataGluA2-gamma2 complex 37 degrees C desensitized state-2 LBD-TMD, locally filtered map
Sample
  • Complex: GluA2-gamma2 complex
    • Protein or peptide: Isoform Flip of Glutamate receptor 2
    • Protein or peptide: TARPgamma2
  • Ligand: GLUTAMIC ACID
Keywordsligand-gated ion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / response to lithium ion ...regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / regulation of receptor recycling / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / cellular response to glycine / immunoglobulin binding / asymmetric synapse / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / conditioned place preference / regulation of synaptic transmission, glutamatergic / response to fungicide / extracellular ligand-gated monoatomic ion channel activity / cytoskeletal protein binding / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / glutamate-gated calcium ion channel activity / somatodendritic compartment / presynaptic active zone membrane / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / excitatory synapse / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / positive regulation of excitatory postsynaptic potential / SNARE binding / dendritic shaft / synaptic membrane / establishment of protein localization / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / long-term synaptic potentiation / receptor internalization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / synaptic vesicle / amyloid-beta binding / presynapse / signaling receptor activity / growth cone / chemical synaptic transmission / scaffold protein binding / presynaptic membrane / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / external side of plasma membrane / axon / neuronal cell body / dendrite / protein kinase binding / synapse / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.52 Å
AuthorsKumar Mondal A / Twomey EC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM154904 United States
CitationJournal: Nature / Year: 2025
Title: Glutamate gating of AMPA-subtype iGluRs at physiological temperatures.
Authors: Anish Kumar Mondal / Elisa Carrillo / Vasanthi Jayaraman / Edward C Twomey /
Abstract: Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that mediate most excitatory neurotransmission. iGluRs are gated by glutamate, where on glutamate binding, they open ...Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that mediate most excitatory neurotransmission. iGluRs are gated by glutamate, where on glutamate binding, they open their ion channels to enable cation influx into postsynaptic neurons, initiating signal transduction. The structural mechanics of how glutamate gating occurs in full-length iGluRs is not well understood. Here, using the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype iGluR (AMPAR), we identify the glutamate-gating mechanism. AMPAR activation by glutamate is augmented at physiological temperatures. By preparing AMPARs for cryogenic-electron microscopy at these temperatures, we captured the glutamate-gating mechanism. Activation by glutamate initiates ion channel opening that involves all ion channel helices hinging away from the pore axis in a motif that is conserved across all iGluRs. Desensitization occurs when the local dimer pairs decouple and enables closure of the ion channel below through restoring the channel hinges and refolding the channel gate. Our findings define how glutamate gates iGluRs, provide foundations for therapeutic design and demonstrate how physiological temperatures can alter iGluR function.
History
DepositionJan 8, 2025-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48559.png

Downloads & links

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Map

FileDownload / File: emd_48559.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluA2-gamma2 complex 37 degrees C desensitized state-2 LBD-TMD, locally filtered map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 440 pix.
= 426.8 Å		0.97 Å/pix.
x 440 pix.
= 426.8 Å		0.97 Å/pix.
x 440 pix.
= 426.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.4291288 - 0.72777337
Average (Standard dev.)0.0008221708 (±0.011154252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: GluA2-gamma2 complex 37 degrees C desensitized state-2 LBD-TMD...

Fileemd_48559_additional_1.map
AnnotationGluA2-gamma2 complex 37 degrees C desensitized state-2 LBD-TMD unsharpened map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: GluA2-gamma2 complex 37 degrees C desensitized state-2 LBD-TMD...

Fileemd_48559_half_map_1.map
AnnotationGluA2-gamma2 complex 37 degrees C desensitized state-2 LBD-TMD half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: GluA2-gamma2 complex 37 degrees C desensitized state-2 LBD-TMD...

Fileemd_48559_half_map_2.map
AnnotationGluA2-gamma2 complex 37 degrees C desensitized state-2 LBD-TMD half map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : GluA2-gamma2 complex

EntireName: GluA2-gamma2 complex
Components
  • Complex: GluA2-gamma2 complex
    • Protein or peptide: Isoform Flip of Glutamate receptor 2
    • Protein or peptide: TARPgamma2
  • Ligand: GLUTAMIC ACID

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Supramolecule #1: GluA2-gamma2 complex

SupramoleculeName: GluA2-gamma2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Macromolecule #1: Isoform Flip of Glutamate receptor 2

MacromoleculeName: Isoform Flip of Glutamate receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 46.074305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EQKTVVVTTI LESPYVMMKK NHEMLEGNER YEGYCVDLAA EIAKHCGFKY KLTIVGDGKY GARDADTKIW NGMVGELVYG KADIAIAPL TITLVREEVI DFSKPFMSLG ISIMIKKPQK SKPGVFSFLD PLAYEIWMCI VFAYIGVSVV LFLVSRFSPY S ESTNEFGI ...String:
EQKTVVVTTI LESPYVMMKK NHEMLEGNER YEGYCVDLAA EIAKHCGFKY KLTIVGDGKY GARDADTKIW NGMVGELVYG KADIAIAPL TITLVREEVI DFSKPFMSLG ISIMIKKPQK SKPGVFSFLD PLAYEIWMCI VFAYIGVSVV LFLVSRFSPY S ESTNEFGI FNSLWFSLGA FMQQGCDISP RSLSGRIVGG VWWFFTLIII SSYTANLAAF LTVERMVSPI ESAEDLSKQT EI AYGTLDS GSTKEFFRRS KIAVFDKMWT YMRSAEPSVF VRTTAEGVAR VRKSKGKYAY LLESTMNEYI EQRKPCDTMK VGG NLDSKG YGIATPKGSS LGTPVNLAVL KLSEQGVLDK LKNKWWYDKG ECGAKDSGSK EKTSALSLSN VAGVFYILVG GLGL AMLVA LIEFCYKSRA

UniProtKB: Glutamate receptor 2

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Macromolecule #2: TARPgamma2

MacromoleculeName: TARPgamma2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.984268 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RGVQMLLTTV GAFAAFSLMT IAVGTDYWLY SRGVCKEVMT HSGLWRTCCL EGNFKGLCKQ IDHFAEYFLR AVRASSIFPI LSVILLFMG GLCIAASEFY KTRHNIILSA GIFFVSAGLS NIIGIIVYIS ANAGNSYSYG WSFYFGALSF IIAEMVGVLA V HMFIDRHK QLTG

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Macromolecule #3: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135708
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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