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- EMDB-53109: The composite map of of the AMPAR complex GluA3- TARP gamma2 in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-53109
TitleThe composite map of of the AMPAR complex GluA3- TARP gamma2 in the apo state.
Map dataComposite map of the AMPAR complex GluA3-TARP gamma 2 in the apo state.
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 / regulation of AMPA receptor activity / channel regulator activity / Trafficking of AMPA receptors / 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 / regulation of AMPA receptor activity / channel regulator activity / Trafficking of AMPA receptors / 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 / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / asymmetric synapse / ionotropic glutamate receptor complex / regulation of receptor recycling / membrane depolarization / Unblocking of NMDA receptors, glutamate binding and activation / synaptic cleft / positive regulation of synaptic transmission, glutamatergic / 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 (rats) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPokharna A / Krieger J / Greger I / Ho H / Yamashita K / Cais O / Singh B
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
DepositionMar 11, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53109.png

Downloads & links

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Map

FileDownload / File: emd_53109.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the AMPAR complex GluA3-TARP gamma 2 in the apo state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.0
Minimum - Maximum-0.7656952 - 66.083619999999996
Average (Standard dev.)1.7437553 (±1.3089122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Low-resolution consensus map of the AMPAR complex GluA3-TARP...

Fileemd_53109_additional_1.map
AnnotationLow-resolution consensus map of the AMPAR complex GluA3-TARP gamma 2 in the apo state corresponding to the composite map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 (rats)

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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: 8 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 131.711859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FPNTISIGGL FMRNTVQEHS AFRFAVQLYN TNQNTTEKPF HLNYHVDHLD SSNSFSVTNA FCSQFSRGVY AIFGFYDQMS MNTLTSFCG ALHTSFVTPS FPTDADVQFV IQMRPALKGA ILSLLSYYKW EKFVYLYDTE RGFSVLQAIM EAAVQNNWQV T ARSVGNIK ...String:
FPNTISIGGL FMRNTVQEHS AFRFAVQLYN TNQNTTEKPF HLNYHVDHLD SSNSFSVTNA FCSQFSRGVY AIFGFYDQMS MNTLTSFCG ALHTSFVTPS FPTDADVQFV IQMRPALKGA ILSLLSYYKW EKFVYLYDTE RGFSVLQAIM EAAVQNNWQV T ARSVGNIK DVQEFRRIIE EMDRRQEKRY LIDCEVERIN TILEQVVILG KHSRGYHYML ANLGFTDILL ERVMHGGANI TG FQIVNNE NPMVQQFIQR WVRLDEREFP EAKNAPLKYT SALTHDAILV IAEAFRYLRR QRVDVSRRGS AGDCLANPAV PWS QGIDIE RALKMVQVQG MTGNIQFDTY GRRTNYTIDV YEMKVSGSRK AGYWNEYERF VPFSDQQISN DSSSSENRTI VVTT ILESP YVMYKKNHEQ LEGNERYEGY CVDLAYEIAK HVRIKYKLSI VGDGKYGARD PETKIWNGMV GELVYGRADI AVAPL TITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVVLFLV SRFSPYEWHL EDNNEE PRD PQSPPDPPNE FGIFNSLWFS LGAFMQQGCD ISPRSLSGRI VGGVWWFFTL IIISSYTANL AAFLTVERMV SPIESAE DL AKQTEIAYGT LDSGSTKEFF RRSKIAVYEK MWSYMKSAEP SVFTKTTADG VARVRKSKGK FAFLLESTMN EYIEQRKP C DTMKVGGNLD SKGYGVATPK GSALGTPVNL AVLKLSEQGI LDKLKNKWWY DKGECGAKDS GSKDKTSALS LSNVAGVFY ILVGGLGLAM MVALIEFCYK SRAESKRMKL TKNTQNFKPA PAGGSGSGGL FDRGVQMLLT TVGAFAAFSL MTIAVGTDYW LYSRGVCKT KSVSENETSK KNEEVMTHSG LWRTCCLEGN FKGLCKQIDH FPEDADYEAD TAEYFLRAVR ASSIFPILSV I LLFMGGLC IAASEFYKTR HNIILSAGIF FVSAGLSNII GIIVYISANA GDPSKSDSKK NSYSYGWSFY FGALSFIIAE MV GVLAVHM FIDRHKQLRA TARATDYLQA SAITRIPSYR YRYQRRSRSS SRSTEPSHSR DASPVGVKGF NTLPSTEISM YTL SRDPLK AATTPTATYN SDRDNSFLQV HNCIQKDSKD SLHANTANRR TTPV

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: GATAN K3 BIOQUANTUM (6k 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: 2.9 Å / Resolution method: OTHER / Number images used: 1184304
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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