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- PDB-9z6u: The structure of TMD with 2 TARPs and 2 CNIHs from all native AMP... -

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Basic information

Entry
Database: PDB / ID: 9z6u
TitleThe structure of TMD with 2 TARPs and 2 CNIHs from all native AMPA receptor subtypes
Components
  • Glutamate receptor 2
  • Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4)
  • Mix of Protein cornichon homolog 2 and 3
  • Voltage-dependent calcium channel gamma-8 subunit
KeywordsMEMBRANE PROTEIN / Ionotropic glutamate receptor AMPA receptor
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
TETRADECANE / DODECANE / Chem-POV / Chem-XVD / Glutamate receptor 2 / Voltage-dependent calcium channel gamma-8 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsPark, J. / Gouaux, E.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4)
B: Glutamate receptor 2
C: Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4)
D: Glutamate receptor 2
E: Mix of Protein cornichon homolog 2 and 3
F: Mix of Protein cornichon homolog 2 and 3
G: Voltage-dependent calcium channel gamma-8 subunit
H: Voltage-dependent calcium channel gamma-8 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,12454
Polymers241,6728
Non-polymers20,45246
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 8 molecules ACBDEFGH

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


Mass: 29723.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Protein Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2


Mass: 29838.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P23819
#3: Protein Mix of Protein cornichon homolog 2 and 3


Mass: 17901.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Protein Voltage-dependent calcium channel gamma-8 subunit / Neuronal voltage-gated calcium channel gamma-8 subunit / Transmembrane AMPAR regulatory protein ...Neuronal voltage-gated calcium channel gamma-8 subunit / Transmembrane AMPAR regulatory protein gamma-8 / TARP gamma-8


Mass: 43371.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VHW2

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Non-polymers , 4 types, 46 molecules

#5: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#6: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C14H30
#7: Chemical ChemComp-XVD / 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol


Mass: 328.674 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8ClF3N2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Native AMPA receptors with 2 TARPs and 2 CNIHs / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 8
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88827 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.24 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00349430
ELECTRON MICROSCOPYf_angle_d0.468612682
ELECTRON MICROSCOPYf_chiral_restr0.0361438
ELECTRON MICROSCOPYf_plane_restr0.00331490
ELECTRON MICROSCOPYf_dihedral_angle_d4.99621412

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