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- PDB-9hpk: Open state TMD-LBD of the GluA3(R439G) with TARP gamma2 -

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Basic information

Entry
Database: PDB / ID: 9hpk
TitleOpen state TMD-LBD of the GluA3(R439G) with TARP gamma2
ComponentsIsoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
KeywordsMEMBRANE PROTEIN / ion channel / glutamate
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / membrane hyperpolarization ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / membrane hyperpolarization / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / protein heterotetramerization / neuromuscular junction development / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / transmission of nerve impulse / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / membrane depolarization / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / synaptic cleft / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / response to fungicide / glutamate-gated receptor activity / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / somatodendritic compartment / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / calcium channel regulator activity / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / dendritic shaft / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / Schaffer collateral - CA1 synapse / long-term synaptic potentiation / terminal bouton / response to calcium ion / amyloid-beta binding / presynaptic membrane / protein homotetramerization / dendritic spine / perikaryon / postsynaptic membrane / postsynaptic density / neuronal cell body / dendrite / glutamatergic synapse / cell surface / protein-containing complex / membrane / plasma membrane
Similarity search - Function
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 / 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-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 / 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 3 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsPokharna, A. / Singh, B. / Krieger, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105174197 United Kingdom
CitationJournal: Nature / Year: 2025
Title: Architecture, dynamics and biogenesis of GluA3 AMPA glutamate receptors.
Authors: Aditya Pokharna / Imogen Stockwell / Josip Ivica / Bishal Singh / Johannes Schwab / Carlos Vega-Gutiérrez / Beatriz Herguedas / Ondrej Cais / James M Krieger / Ingo H Greger /
Abstract: AMPA-type glutamate receptors (AMPARs) mediate the majority of excitatory neurotransmission in the brain. Assembled from combinations of four core subunits, GluA1-4, and ~20 auxiliary subunits, their ...AMPA-type glutamate receptors (AMPARs) mediate the majority of excitatory neurotransmission in the brain. Assembled from combinations of four core subunits, GluA1-4, and ~20 auxiliary subunits, their molecular diversity tunes information transfer and storage in a brain circuit-specific manner. GluA3, a subtype strongly associated with disease, functions as both a fast transmitting Ca-permeable (CP) AMPAR at sensory synapses, and as a Ca-impermeable (CI) receptor at cortical synapses. Here, we present cryo-EM structures of the CP GluA3 homomer, which substantially diverge from other AMPARs. The GluA3 extracellular domain tiers (NTD and LBD) are closely coupled throughout gating states, creating previously unseen interfaces that impact signalling and harbour human disease mutations. Central to this architecture is a stacking interaction between two arginine residues (Arg163) in the NTD dimer interface, trapping a unique NTD dimer conformation that enables close contacts with the LBD. Rupture of the Arg163 stack not only alters the structure and dynamics of the GluA3 extracellular region, but also increases receptor trafficking, and the expression of GluA3 heteromers at the synapse. We further show that a mammalian-specific GluA3 trafficking checkpoint determines conformational stability of the LBD tier. Hence, specific design features define communication and biogenesis of GluA3, offering a framework to interrogate this disease-prone glutamate receptor.
History
DepositionDec 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
B: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
C: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
D: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
W: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
X: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
Y: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
Z: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit


Theoretical massNumber of molelcules
Total (without water)1,062,1278
Polymers1,062,1278
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit / GluR-3 / AMPA-selective glutamate receptor 3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / ...GluR-3 / AMPA-selective glutamate receptor 3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / AMPA 3 / Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin / Transmembrane AMPAR regulatory protein gamma-2 / TARP gamma-2


Mass: 132765.891 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria3, GluA3, Glur3, Cacng2, Stg / Cell line (production host): EXPI293F / Production host: Homo sapiens (human) / References: UniProt: P19492, UniProt: Q71RJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
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: GluA3 in tandem with TARP gamma2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Cell: expi293f
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: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 37.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280853 / Symmetry type: POINT

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