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- PDB-9zkt: The TMD structure of native mouse AMPAR with 2 TARPs 2 CNIHs and ... -

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Basic information

Entry
Database: PDB / ID: 9zkt
TitleThe TMD structure of native mouse AMPAR with 2 TARPs 2 CNIHs and PRRT1/SynDIG4
Components
  • (Glutamate receptor ...) x 2
  • Proline-rich transmembrane protein 1
  • Protein cornichon homolog 2
  • Voltage-dependent calcium channel gamma-8 subunit
KeywordsSIGNALING PROTEIN / iGluR / AMPA receptors
Function / homology
Function and homology information


negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / Activation of AMPA receptors / COPII-mediated vesicle transport / Synaptic adhesion-like molecules / LGI-ADAM interactions / Unblocking of NMDA receptors, glutamate binding and activation ...negative regulation of receptor localization to synapse / negative regulation of anterograde synaptic vesicle transport / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Cargo concentration in the ER / Activation of AMPA receptors / COPII-mediated vesicle transport / Synaptic adhesion-like molecules / LGI-ADAM interactions / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors / cellular response to ammonium ion / axonal spine / positive regulation of locomotion involved in locomotory behavior / Trafficking of AMPA receptors / positive regulation of membrane potential / localization within membrane / response to sucrose / signaling receptor regulator activity / L-type voltage-gated calcium channel complex / regulation of monoatomic ion transmembrane transport / myosin V binding / positive regulation of AMPA receptor activity / neuron spine / postsynaptic neurotransmitter receptor diffusion trapping / proximal dendrite / protein phosphatase 2B binding / response to arsenic-containing substance / regulation of AMPA receptor activity / cellular response to L-glutamate / channel regulator activity / protein localization to cell surface / cellular response to dsRNA / long-term synaptic depression / ligand-gated calcium channel activity / dendritic spine membrane / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / cellular response to amine stimulus / response to morphine / response to psychosocial stress / peptide hormone receptor binding / perisynaptic space / spinal cord development / neuronal cell body membrane / protein kinase A binding / response to lithium ion / AMPA glutamate receptor activity / behavioral response to pain / transmission of nerve impulse / regulation of receptor recycling / immunoglobulin binding / adenylate cyclase binding / AMPA glutamate receptor complex / response to electrical stimulus / ionotropic glutamate receptor complex / asymmetric synapse / G-protein alpha-subunit binding / glutamate receptor binding / positive regulation of synaptic transmission / conditioned place preference / long-term memory / regulation of postsynaptic membrane neurotransmitter receptor levels / neuronal action potential / voltage-gated calcium channel activity / postsynaptic density, intracellular component / response to fungicide / vesicle-mediated transport / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / somatodendritic compartment / synapse assembly / presynaptic active zone membrane / ionotropic glutamate receptor binding / dendrite membrane / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / dendritic shaft / synaptic membrane / response to cocaine / PDZ domain binding / calcium channel regulator activity / neuromuscular junction / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / receptor internalization / regulation of membrane potential / cerebral cortex development / regulation of synaptic plasticity / synapse organization / response to nutrient levels / recycling endosome / postsynaptic density membrane / modulation of chemical synaptic transmission / response to toxic substance / long-term synaptic potentiation / Schaffer collateral - CA1 synapse
Similarity search - Function
CD225/Dispanin family / : / Interferon-induced transmembrane protein / Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / Voltage-dependent calcium channel, gamma-8 subunit / : ...CD225/Dispanin family / : / Interferon-induced transmembrane protein / Cornichon / Cornichon, conserved site / Cornichon protein / Cornichon family signature. / Cornichon / 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 / 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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / Chem-POV / Glutamate receptor / Protein cornichon homolog 2 / Proline-rich transmembrane protein 1 / Glutamate receptor 1 / Voltage-dependent calcium channel gamma-8 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsFang, C.L. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Adv / Year: 2026
Title: Native AMPA receptor architecture reveals SynDIG4 engagement and auxiliary subunit heterogeneity.
Authors: Chengli Fang / Eric Gouaux /
Abstract: AMPA-type glutamate receptors (AMPARs) are complex assemblies whose compositional heterogeneity underlies diverse excitatory signaling in the mammalian brain. Here, we determine high-resolution cryo- ...AMPA-type glutamate receptors (AMPARs) are complex assemblies whose compositional heterogeneity underlies diverse excitatory signaling in the mammalian brain. Here, we determine high-resolution cryo-electron microscopy (cryo-EM) structures of native AMPAR complexes rapidly purified from mouse brain. These structures capture receptors in physiologically relevant assemblies containing distinct combinations of transmembrane AMPA receptor regulatory protein (TARP) and cornichon homolog (CNIH) auxiliary subunits and reveal unambiguous density for the brain-specific protein SynDIG4. The resolved topology and interaction network of SynDIG4 show that it engages the receptor through a CNIH-dependent interface and occupies a position adjacent to structural elements of GluA1 implicated in trafficking and synaptic plasticity. The diversity of auxiliary stoichiometries observed across native complexes highlights a flexible organizational scheme through which AMPARs incorporate distinct regulatory partners. These findings illuminate the organization of native AMPAR assemblies and define the structural context for SynDIG4 function in the mammalian brain.
History
DepositionDec 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 1
B: Glutamate receptor 2
C: Glutamate receptor 1
D: Glutamate receptor 2
E: Protein cornichon homolog 2
F: Protein cornichon homolog 2
G: Voltage-dependent calcium channel gamma-8 subunit
H: Voltage-dependent calcium channel gamma-8 subunit
M: Proline-rich transmembrane protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,10727
Polymers371,0799
Non-polymers7,02818
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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Glutamate receptor ... , 2 types, 4 molecules ACBD

#1: Protein Glutamate receptor 1 / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / ...GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / AMPA 1 / GluA1


Mass: 55260.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mix of AMPAR subunits (GluA1, GluA3, and GluA4) / Source: (natural) Mus musculus (house mouse) / References: UniProt: P23818
#2: Protein Glutamate receptor 2


Mass: 52118.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: C9K0Z0

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Protein , 3 types, 5 molecules EFGHM

#3: Protein Protein cornichon homolog 2 / CNIH-2 / Cornichon family AMPA receptor auxiliary protein 2 / Cornichon-like protein


Mass: 18949.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O35089
#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: 43502.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VHW2
#5: Protein Proline-rich transmembrane protein 1 / Dispanin subfamily D member 1 / DSPD1 / Synapse differentiation-induced protein 4 / SynDIG4


Mass: 31416.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O35449

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Non-polymers , 3 types, 18 molecules

#6: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2
#7: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestN
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 mouse AMPAR / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 8
SpecimenEmbedding 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: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38978 / Symmetry type: POINT
RefinementHighest resolution: 3.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049788
ELECTRON MICROSCOPYf_angle_d0.7413187
ELECTRON MICROSCOPYf_dihedral_angle_d6.1031606
ELECTRON MICROSCOPYf_chiral_restr0.0441523
ELECTRON MICROSCOPYf_plane_restr0.0051537

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