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- EMDB-71409: Active substate 4 of the GluA4 homotetramer. -

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Basic information

Entry
Database: EMDB / ID: EMD-71409
TitleActive substate 4 of the GluA4 homotetramer.
Map dataMap corresponding to GluA4 active substate 4.
Sample
  • Complex: Octameric complex of four GluA4 subunits in complex with four TARP gamma 2 subunits.
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
    • Protein or peptide: Isoform 2 of Glutamate receptor 4
  • Ligand: GLUTAMIC ACID
  • Ligand: CYCLOTHIAZIDE
KeywordsAMPAR / Ion Channel / Glutamate Receptor / Ligand-gated / MEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / Trafficking of AMPA receptors / 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 / Trafficking of AMPA receptors / kainate selective glutamate receptor complex ...Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / Trafficking of AMPA receptors / 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 / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / membrane hyperpolarization / regulation of synapse structure or activity / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / Activation of AMPA receptors / neuromuscular junction development / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / negative regulation of smooth muscle cell apoptotic process / transmission of nerve impulse / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / membrane depolarization / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission, glutamatergic / regulation of postsynaptic membrane neurotransmitter receptor levels / response to fungicide / voltage-gated calcium channel activity / glutamate-gated receptor 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 / regulation of membrane potential / 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 / terminal bouton / dendritic spine / chemical synaptic transmission / postsynaptic density / neuronal cell body / dendrite / synapse / glutamatergic synapse / cell surface / identical protein binding / 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
Voltage-dependent calcium channel gamma-2 subunit / Glutamate receptor 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsHale WD / Huganir RL / Twomey EC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)K99MH132811 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R37NS036715 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM154904 United States
CitationJournal: To Be Published
Title: Conformational Plasticity Tunes the GluA4 Channel Gate
Authors: Hale WD / Huganir RL / Twomey EC
History
DepositionJun 24, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71409.png

Downloads & links

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Map

FileDownload / File: emd_71409.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap corresponding to GluA4 active substate 4.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.16006279 - 0.34667665
Average (Standard dev.)0.0007388532 (±0.010469915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A corresponding to GluA4 active substate 4.

Fileemd_71409_half_map_1.map
AnnotationHalf map A corresponding to GluA4 active substate 4.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B corresponding to GluA4 active substate 4.

Fileemd_71409_half_map_2.map
AnnotationHalf map B corresponding to GluA4 active substate 4.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Octameric complex of four GluA4 subunits in complex with four TAR...

EntireName: Octameric complex of four GluA4 subunits in complex with four TARP gamma 2 subunits.
Components
  • Complex: Octameric complex of four GluA4 subunits in complex with four TARP gamma 2 subunits.
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
    • Protein or peptide: Isoform 2 of Glutamate receptor 4
  • Ligand: GLUTAMIC ACID
  • Ligand: CYCLOTHIAZIDE

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Supramolecule #1: Octameric complex of four GluA4 subunits in complex with four TAR...

SupramoleculeName: Octameric complex of four GluA4 subunits in complex with four TARP gamma 2 subunits.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Isoform 2 of Glutamate receptor 4

MacromoleculeName: Isoform 2 of Glutamate receptor 4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 95.140234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGKIMHISVL LSPVLWGLIF GVSSVQIGGL FIRNTDQEYT AFRLAIFLHN TSPNASEAPF NLVPHVDNIE TANSFAVTNA FCSQYSRGV FAIFGLYDKR SVHTLTSFCS ALHISLITPS FPTEGESQFV LQLRPSLRGA LLSLLDHYEW NCFVFLYDTD R GYSILQAI ...String:
MGKIMHISVL LSPVLWGLIF GVSSVQIGGL FIRNTDQEYT AFRLAIFLHN TSPNASEAPF NLVPHVDNIE TANSFAVTNA FCSQYSRGV FAIFGLYDKR SVHTLTSFCS ALHISLITPS FPTEGESQFV LQLRPSLRGA LLSLLDHYEW NCFVFLYDTD R GYSILQAI MEKAGQNGWH VSAICVENFN DVSYRQLLEE LDRRQEKKFV IDCEIERLQN ILEQIVSVGK HVKGYHYIIA NL GFKDISL ERFIHGGANV TGFQLVDFNT PMVTKLMDRW KKLDQREYPG SETPPKYTSA LTYDGVLVMA ETFRSLRRQK IDI SRRGNA GDCLANPAAP WGQGIDMERT LKQVRIQGLT GNVQFDHYGR RVNYTMDVFE LKSTGPRKVG YWNDMDKLVL IQDM PTLGN DTAAIENRTV VVTTIMESPY VMYKKNHEMF EGNDKYEGYC VDLASEIAKH IGIKYKIAIV PDGKYGARDA DTKIW NGMV GELVYGKAEI AIAPLTITLV REEVIDFSKP FMSLGISIMI KKPQKSKPGV FSFLDPLAYE IWMCIVFAYI GVSVVL FLV SRFSPYEWHT EEPEDGKEGP SDQPPNEFGI FNSLWFSLGA FMQQGCDISP RSLSGRIVGG VWWFFTLIII SSYTANL AA FLTVERMVSP IESAEDLAKQ TEIAYGTLDS GSTKEFFRRS KIAVYEKMWT YMRSAEPSVF TRTTAEGVAR VRKSKGKF A FLLESTMNEY IEQRKPCDTM KVGGNLDSKG YGVATPKGSS LRTPVNLAVL KLSEAGVLDK LKNKWWYDKG ECGPKDSGS KDKTSALSLS NVAGVFYILV GGLGLAMLVA LIEFCYKSRA EAKRMK

UniProtKB: Glutamate receptor 4

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Macromolecule #2: Voltage-dependent calcium channel gamma-2 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-2 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.066498 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFDRGVQML LTTVGAFAAF SLMTIAVGTD YWLYSRGVCK TKSVSEDETS KKNEEVMTHS GLWRTCCLEG NFKGLCKQID HFPEDADYE ADTAEYFLRA VRASSIFPIL SVILLFMGGL CIAASEFYKT RHNIILSAGI FFVSAGLSNI IGIIVYISAN A GDPSKSDS ...String:
GLFDRGVQML LTTVGAFAAF SLMTIAVGTD YWLYSRGVCK TKSVSEDETS KKNEEVMTHS GLWRTCCLEG NFKGLCKQID HFPEDADYE ADTAEYFLRA VRASSIFPIL SVILLFMGGL CIAASEFYKT RHNIILSAGI FFVSAGLSNI IGIIVYISAN A GDPSKSDS KKNSYSYGWS FYFGALSFII AEMVGVLAVH MFIDRHKQLT G

UniProtKB: Voltage-dependent calcium channel gamma-2 subunit

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Macromolecule #3: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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Macromolecule #4: CYCLOTHIAZIDE

MacromoleculeName: CYCLOTHIAZIDE / type: ligand / ID: 4 / Number of copies: 4 / Formula: CYZ
Molecular weightTheoretical: 389.878 Da
Chemical component information

ChemComp-CYZ:
CYCLOTHIAZIDE

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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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 59237
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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