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- EMDB-52329: The NTD dimer and the interfacing LBD region of the AMPAR complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-52329
TitleThe NTD dimer and the interfacing LBD region of the AMPAR complex GluA3(R439G,R163I)- TARP gamma2 in the apo state.
Map data
Sample
  • Complex: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
    • Protein or peptide: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
KeywordsAMPAR / ion channels / neurotransmission / MEMBRANE PROTEIN
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 / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / LGI-ADAM interactions / membrane hyperpolarization ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / LGI-ADAM interactions / membrane hyperpolarization / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / voltage-gated calcium channel complex / protein heterotetramerization / neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / positive regulation of synaptic transmission, glutamatergic / synaptic cleft / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / response to fungicide / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / hippocampal mossy fiber to CA3 synapse / dendritic shaft / regulation of membrane potential / calcium channel regulator activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / response to calcium ion / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / long-term synaptic potentiation / terminal bouton / amyloid-beta binding / presynaptic membrane / perikaryon / protein homotetramerization / dendritic spine / 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 (rat) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsPokharna A / Krieger J / Greger I / Ho H / Yamashita K / Cais O
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust223194/Z/21/Z United Kingdom
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 around 20 auxiliary subunits, ...AMPA-type glutamate receptors (AMPARs) mediate the majority of excitatory neurotransmission in the brain. Assembled from combinations of four core subunits, GluA1-4 and around 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 AMPAR at sensory synapses, and as a Ca-impermeable receptor at cortical synapses. Here we present cryo-electron microscopy structures of the Ca-permeable GluA3 homomer, which substantially diverges from other AMPARs. The GluA3 extracellular domain tiers (N-terminal domain (NTD) and ligand-binding domain (LBD)) are closely coupled throughout gating states, creating interfaces that impact signalling and contain human disease-associated 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 the conformational stability of the LBD tier. Thus, specific design features define communication and biogenesis of GluA3, offering a framework to examine this disease-associated glutamate receptor.
History
DepositionDec 12, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52329.png

Downloads & links

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Map

FileDownload / File: emd_52329.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 512 pix.
= 488.96 Å		0.96 Å/pix.
x 512 pix.
= 488.96 Å		0.96 Å/pix.
x 512 pix.
= 488.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.955 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-47.225825999999998 - 70.566283999999996
Average (Standard dev.)-0.000000000002263 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 488.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52329_half_map_1.map
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Half map: #1

Fileemd_52329_half_map_2.map
Projections & Slices
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Sample components

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Entire : homomeric AMPAR complex GluA3 in tandem with the auxiliary subuni...

EntireName: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
Components
  • Complex: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
    • Protein or peptide: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit

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Supramolecule #1: homomeric AMPAR complex GluA3 in tandem with the auxiliary subuni...

SupramoleculeName: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus (rat)

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Macromolecule #1: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium ch...

MacromoleculeName: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 132.621688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDYKDDDDKF PNTISIGGLF MRNTVQEHSA FRFAVQLYNT NQNTTEKPFH LNYHVDHLDS SNSFSVTNAF CSQFSRGVYA IFGFYDQMS MNTLTSFCGA LHTSFVTPSF PTDADVQFVI QMRPALKGAI LSLLSYYKWE KFVYLYDTER GFSVLQAIME A AVQNNWQV ...String:
GDYKDDDDKF PNTISIGGLF MRNTVQEHSA FRFAVQLYNT NQNTTEKPFH LNYHVDHLDS SNSFSVTNAF CSQFSRGVYA IFGFYDQMS MNTLTSFCGA LHTSFVTPSF PTDADVQFVI QMRPALKGAI LSLLSYYKWE KFVYLYDTER GFSVLQAIME A AVQNNWQV TAISVGNIKD VQEFRRIIEE MDRRQEKRYL IDCEVERINT ILEQVVILGK HSRGYHYMLA NLGFTDILLE RV MHGGANI TGFQIVNNEN PMVQQFIQRW VRLDEREFPE AKNAPLKYTS ALTHDAILVI AEAFRYLRRQ RVDVSRRGSA GDC LANPAV PWSQGIDIER ALKMVQVQGM TGNIQFDTYG RRTNYTIDVY EMKVSGSRKA GYWNEYERFV PFSDQQISND SSSS ENRTI VVTTILESPY VMYKKNHEQL EGNERYEGYC VDLAYEIAKH VGIKYKLSIV GDGKYGARDP ETKIWNGMVG ELVYG RADI AVAPLTITLV REEVIDFSKP FMSLGISIMI KKPQKSKPGV FSFLDPLAYE IWMCIVFAYI GVSVVLFLVS RFSPYE WHL EDNNEEPRDP QSPPDPPNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTANLA AFLTVER MV SPIESAEDLA KQTEIAYGTL DSGSTKEFFR RSKIAVYEKM WSYMKSAEPS VFTKTTADGV ARVRKSKGKF AFLLESTM N EYIEQRKPCD TMKVGGNLDS KGYGVATPKG SALGTPVNLA VLKLSEQGIL DKLKNKWWYD KGECGAKDSG SKDKTSALS LSNVAGVFYI LVGGLGLAMM VALIEFCYKS RAESKRMKLT KNTQNFKPAP AGGSGSGGLF DRGVQMLLTT VGAFAAFSLM TIAVGTDYW LYSRGVCKTK SVSENETSKK NEEVMTHSGL WRTCCLEGNF KGLCKQIDHF PEDADYEADT AEYFLRAVRA S SIFPILSV ILLFMGGLCI AASEFYKTRH NIILSAGIFF VSAGLSNIIG IIVYISANAG DPSKSDSKKN SYSYGWSFYF GA LSFIIAE MVGVLAVHMF IDRHKQLRAT ARATDYLQAS AITRIPSYRY RYQRRSRSSS RSTEPSHSRD ASPVGVKGFN TLP STEISM YTLSRDPLKA ATTPTATYNS DRDNSFLQVH NCIQKDSKDS LHANTANRRT TPV

UniProtKB: Glutamate receptor 3, Voltage-dependent calcium channel gamma-2 subunit

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 151985
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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