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- PDB-9zkm: The LBD-TMD structure of native mouse AMPAR with 4 TARPs -

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Basic information

Entry
Database: PDB / ID: 9zkm
TitleThe LBD-TMD structure of native mouse AMPAR with 4 TARPs
Components
  • (Glutamate receptor ...) x 2
  • (Voltage-dependent calcium channel gamma- ...) x 2
KeywordsSIGNALING PROTEIN / iGluR / AMPA receptors
Function / homology
Function and homology information


Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Activation of AMPA receptors / Cargo concentration in the ER / COPII-mediated vesicle transport / Presynaptic depolarization and calcium channel opening / Synaptic adhesion-like molecules / LGI-ADAM interactions / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors ...Phase 0 - rapid depolarisation / Phase 2 - plateau phase / Activation of AMPA receptors / Cargo concentration in the ER / COPII-mediated vesicle transport / Presynaptic depolarization and calcium channel opening / Synaptic adhesion-like molecules / LGI-ADAM interactions / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors / axonal spine / positive regulation of locomotion involved in locomotory behavior / Trafficking of AMPA receptors / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion / response to sucrose / L-type voltage-gated calcium channel complex / myosin V binding / cerebellar mossy fiber / neuron spine / postsynaptic neurotransmitter receptor diffusion trapping / proximal dendrite / regulation of AMPA receptor activity / protein phosphatase 2B binding / response to arsenic-containing substance / regulation of monoatomic ion transmembrane transport / channel regulator activity / cellular response to L-glutamate / ligand-gated calcium channel activity / cellular response to dsRNA / membrane hyperpolarization / nervous system process / dendritic spine membrane / beta-2 adrenergic receptor binding / long-term synaptic depression / protein targeting to membrane / cellular response to peptide hormone stimulus / voltage-gated calcium channel complex / cellular response to amine stimulus / peptide hormone receptor binding / response to psychosocial stress / neurotransmitter receptor localization to postsynaptic specialization membrane / response to morphine / perisynaptic space / spinal cord development / neuronal cell body membrane / neuromuscular junction development / protein kinase A binding / response to lithium ion / AMPA glutamate receptor activity / transmission of nerve impulse / immunoglobulin binding / adenylate cyclase binding / behavioral response to pain / AMPA glutamate receptor complex / regulation of receptor recycling / response to electrical stimulus / ionotropic glutamate receptor complex / asymmetric synapse / G-protein alpha-subunit binding / glutamate receptor binding / membrane depolarization / conditioned place preference / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / long-term memory / voltage-gated calcium channel activity / postsynaptic density, intracellular component / response to fungicide / neuronal action potential / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / positive regulation of synaptic transmission, glutamatergic / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / synapse assembly / excitatory synapse / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / dendritic shaft / synaptic membrane / PDZ domain binding / calcium channel regulator activity / response to cocaine / neuromuscular junction / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / regulation of membrane potential / response to nutrient levels / cerebral cortex development / response to calcium ion / receptor internalization / regulation of synaptic plasticity / recycling endosome
Similarity search - Function
Voltage-dependent calcium channel, gamma-8 subunit / Voltage-dependent calcium channel, gamma-2 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 ...Voltage-dependent calcium channel, gamma-8 subunit / Voltage-dependent calcium channel, gamma-2 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 / Voltage-dependent calcium channel gamma-2 subunit / 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: 3.13 Å
AuthorsFang, C.L. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Native AMPA receptor architecture reveals SynDIG4 engagement and auxiliary subunit heterogeneity
Authors: Fang, C.L. / Gouaux, E.
History
DepositionDec 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 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: Glutamate receptor 1
B: Glutamate receptor 2
C: Glutamate receptor 1
D: Glutamate receptor 2
E: Voltage-dependent calcium channel gamma-2 subunit
F: Voltage-dependent calcium channel gamma-2 subunit
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)385,65136
Polymers373,6418
Non-polymers12,01028
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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Voltage-dependent calcium channel gamma- ... , 2 types, 4 molecules EFGH

#3: Protein Voltage-dependent calcium channel gamma-2 subunit / Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin / Transmembrane AMPAR regulatory ...Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin / Transmembrane AMPAR regulatory protein gamma-2 / TARP gamma-2


Mass: 35938.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O88602
#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

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Non-polymers , 3 types, 28 molecules

#5: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


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


Mass: 760.076 Da / Num. of mol.: 8 / 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 AMPAR / Type: COMPLEX / Entity ID: #1-#4 / 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: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112093 / Symmetry type: POINT
RefinementHighest resolution: 3.13 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318170
ELECTRON MICROSCOPYf_angle_d0.72524499
ELECTRON MICROSCOPYf_dihedral_angle_d6.1392996
ELECTRON MICROSCOPYf_chiral_restr0.0472791
ELECTRON MICROSCOPYf_plane_restr0.0062966

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