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- PDB-9z6v: The structure of TMD with 3 TARPs and 1 CNIH from all native AMPA... -

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Basic information

Entry
Database: PDB / ID: 9z6v
TitleThe structure of TMD with 3 TARPs and 1 CNIH 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
  • Mix of voltage-dependent calcium channel gamma subunits
  • 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 / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / LGI-ADAM interactions / Trafficking of AMPA receptors / L-type voltage-gated calcium channel complex / regulation of AMPA receptor activity / spine synapse ...Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / LGI-ADAM interactions / Trafficking of AMPA receptors / L-type voltage-gated calcium channel complex / regulation of AMPA receptor activity / spine synapse / dendritic spine cytoplasm / dendritic spine neck / dendritic spine head / ligand-gated monoatomic cation channel activity / perisynaptic space / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / kainate selective glutamate receptor activity / immunoglobulin binding / asymmetric synapse / AMPA glutamate receptor complex / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / cellular response to glycine / conditioned place preference / glutamate receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of synaptic transmission, glutamatergic / cytoskeletal protein binding / glutamate-gated receptor activity / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor binding / dendrite membrane / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / synaptic membrane / dendritic shaft / SNARE binding / calcium channel regulator activity / PDZ domain binding / synaptic transmission, glutamatergic / protein tetramerization / establishment of protein localization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / receptor internalization / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / calcium channel activity / terminal bouton / synaptic vesicle / synaptic vesicle membrane / amyloid-beta binding / presynapse / signaling receptor activity / growth cone / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / external side of plasma membrane / axon / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / 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 / 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: 3 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 voltage-dependent calcium channel gamma subunits
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)263,55036
Polymers244,8158
Non-polymers18,73428
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 , 5 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.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Protein Mix of voltage-dependent calcium channel gamma subunits


Mass: 21045.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: 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 , 3 types, 28 molecules

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


Mass: 760.076 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#7: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30
#8: 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

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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 3 TARPs and 1 CNIH / Type: COMPLEX / Entity ID: #1-#5 / 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
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82389 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 61.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00358981
ELECTRON MICROSCOPYf_angle_d0.467312133
ELECTRON MICROSCOPYf_chiral_restr0.03511402
ELECTRON MICROSCOPYf_plane_restr0.00331438
ELECTRON MICROSCOPYf_dihedral_angle_d3.951312

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