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- EMDB-73861: The structure of TMD with 2 TARPs and 2 CNIHs from all native AMP... -

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Basic information

Entry
Database: EMDB / ID: EMD-73861
TitleThe structure of TMD with 2 TARPs and 2 CNIHs from all native AMPA receptor subtypes
Map data
Sample
  • Complex: Native AMPA receptors with 2 TARPs and 2 CNIHs
    • Protein or peptide: Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4)
    • Protein or peptide: Glutamate receptor 2
    • Protein or peptide: Mix of Protein cornichon homolog 2 and 3
    • Protein or peptide: Voltage-dependent calcium channel gamma-8 subunit
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: TETRADECANE
  • Ligand: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
  • Ligand: DODECANE
KeywordsIonotropic glutamate receptor AMPA receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Activation of AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors / LGI-ADAM interactions / Trafficking of AMPA receptors / L-type voltage-gated calcium channel complex / regulation of AMPA receptor activity / perisynaptic space ...Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Activation of AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors / LGI-ADAM interactions / Trafficking of AMPA receptors / L-type voltage-gated calcium channel complex / regulation of AMPA receptor activity / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / regulation of postsynaptic membrane neurotransmitter receptor levels / glutamate-gated receptor activity / somatodendritic compartment / synaptic membrane / calcium channel regulator activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / Schaffer collateral - CA1 synapse / calcium channel activity / synaptic vesicle / synaptic vesicle membrane / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / dendrite / synapse / glutamatergic synapse / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, gamma-8 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / 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 ...Voltage-dependent calcium channel, gamma-8 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / 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 2 / Voltage-dependent calcium channel gamma-8 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsPark J / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS038631 United States
CitationJournal: Protein Sci / Year: 2026
Title: Efficient and rapid isolation of native AMPA receptor complexes for cryo-EM.
Authors: Jumi Park / Eric Gouaux /
Abstract: Isolating native ion channels for structural characterization is routinely achieved by extraction from membrane fractions of tissue with prolonged mild detergent treatment. AMPA receptors (AMPARs), ...Isolating native ion channels for structural characterization is routinely achieved by extraction from membrane fractions of tissue with prolonged mild detergent treatment. AMPA receptors (AMPARs), glutamatergic receptors that mediate fast excitatory transmission and synaptic plasticity, are coassembled with diverse auxiliary subunits and transiently-interacting partners to finely regulate processes from trafficking to gating kinetics. Previous studies of the composition and architecture of native AMPARs (nAMPARs) isolated from membrane fractions of rodent brain tissue have revealed many different subunit compositions and non-stochastic assemblies of the auxiliary subunits. However, elucidating the molecular architectures of nAMPARs complexed with less populated or transiently bound proteins has proven challenging. Here, we employ strategies for the rapid solubilization and purification of nAMPARs to increase the likelihood of isolating the greatest range of nAMPARs complexes. By utilizing whole brain tissue and reducing solubilization and purification duration, we purify nAMPARs complexed with a wider variety of auxiliary subunits and binding partners in a sufficient quantity and purity for cryo-electron microscopy studies. We resolve previously unreported subunit compositions and conformations that include ones with a half-splayed ATD layer, as well as complexes with four distinct auxiliary subunit arrangements in the TMD layer.
History
DepositionNov 14, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73861.png

Downloads & links

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Map

FileDownload / File: emd_73861.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 429.568 Å		0.84 Å/pix.
x 512 pix.
= 429.568 Å		0.84 Å/pix.
x 512 pix.
= 429.568 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3651357 - 0.7084688
Average (Standard dev.)0.00047143176 (±0.011649985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 429.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73861_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73861_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : Native AMPA receptors with 2 TARPs and 2 CNIHs

EntireName: Native AMPA receptors with 2 TARPs and 2 CNIHs
Components
  • Complex: Native AMPA receptors with 2 TARPs and 2 CNIHs
    • Protein or peptide: Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4)
    • Protein or peptide: Glutamate receptor 2
    • Protein or peptide: Mix of Protein cornichon homolog 2 and 3
    • Protein or peptide: Voltage-dependent calcium channel gamma-8 subunit
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: TETRADECANE
  • Ligand: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
  • Ligand: DODECANE

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Supramolecule #1: Native AMPA receptors with 2 TARPs and 2 CNIHs

SupramoleculeName: Native AMPA receptors with 2 TARPs and 2 CNIHs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4)

MacromoleculeName: Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.723635 KDa
SequenceString: KPGVFSFLDP LAYEIWMCIV FAYIGVSVVL FLVSRFS(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)N EFGIFNSLWF SLGA FMQQG CDISPRSLSG ...String:
KPGVFSFLDP LAYEIWMCIV FAYIGVSVVL FLVSRFS(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)N EFGIFNSLWF SLGA FMQQG CDISPRSLSG RIVGGVWWFF TLIIISSYTA NLAAFLTVER MV(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)SALS LSNVAGVFYI LAGGLGLAMA VALIEFCYKS RA

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Macromolecule #2: Glutamate receptor 2

MacromoleculeName: Glutamate receptor 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.83883 KDa
SequenceString: KPGVFSFLDP LAYEIWMCIV FAYIGVSVVL FLVSRFS(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)N EFGIFNSLWF SLGA FMRQG CDISPRSLSG ...String:
KPGVFSFLDP LAYEIWMCIV FAYIGVSVVL FLVSRFS(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)N EFGIFNSLWF SLGA FMRQG CDISPRSLSG RIVGGVWWFF TLIIISSYTA NLAAFLTVER MV(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)TSALS LSNVAGVFYI LVGGLGLAML VALIEFCYKS RA

UniProtKB: Glutamate receptor 2, Glutamate receptor 2, Glutamate receptor 2

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Macromolecule #3: Mix of Protein cornichon homolog 2 and 3

MacromoleculeName: Mix of Protein cornichon homolog 2 and 3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 17.901887 KDa
SequenceString:
AFTFAAFCYM LALVLCAALI FFAIWHIIAF DELRTDFKAP IDQANPAAAR ERLANIERIC ALLRKLVAPE YSIHALFCAM FLCAAEWAT LGLNAPLLFY HAWRYFHAPA DASEAAYDAA AAMNADALAY CQKEAWCKLA FYLLSFFYYL YAMAYTLVSA

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Macromolecule #4: Voltage-dependent calcium channel gamma-8 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-8 subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 43.371742 KDa
SequenceString: ESLKRWNEER GLWCEKGVQV LLTTIGAFSA FGLMTIAIST DYWLYTRALI CNTTNLTAGD DGPPHRGGSG SSEKKDPGGL THSGLWRIC CLEGLKRGVC VKINHFPEDT DYDHDSAEYL LRVVRASSIF PILSAILLLL GGVCVAASRV YKSKRNIILG A GILFVAAG ...String:
ESLKRWNEER GLWCEKGVQV LLTTIGAFSA FGLMTIAIST DYWLYTRALI CNTTNLTAGD DGPPHRGGSG SSEKKDPGGL THSGLWRIC CLEGLKRGVC VKINHFPEDT DYDHDSAEYL LRVVRASSIF PILSAILLLL GGVCVAASRV YKSKRNIILG A GILFVAAG LSNIIGVIVY ISANAGEPGP KRDEEKKNHY SYGWSFYFGG LSFILAEVIG VLAVNIYIER SREAHCQSRS DL LKAGGGA GGSGGSGPSA ILRLPSYRFR YRRRSRSSSR GSSEASPSRD ASPGGPGGPG FASTDISMYT LSRDPSKGSV AAG LASAGG GGSGAGVGAY GGAAGAAGGG GAGSERDRGS SAGFLTLHNA FPKEAASGVT VTVTGPPAAP APAPAPPAPA APAP GTLSK EAAASNTNTL NRKTTPV

UniProtKB: Voltage-dependent calcium channel gamma-8 subunit

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Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 5 / Number of copies: 20 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #6: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 6 / Number of copies: 18 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #7: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol

MacromoleculeName: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
type: ligand / ID: 7 / Number of copies: 2 / Formula: XVD
Molecular weightTheoretical: 328.674 Da
Chemical component information

ChemComp-XVD:
6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol

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Macromolecule #8: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 8 / Number of copies: 6 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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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

Concentration0.12 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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 / Nominal defocus max: 2.2 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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 88827
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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