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- EMDB-49726: The structure of GluA1/A4 LBD-TMD with 2 TARPs -

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Basic information

Entry
Database: EMDB / ID: EMD-49726
TitleThe structure of GluA1/A4 LBD-TMD with 2 TARPs
Map data
Sample
  • Complex: CP-AMPA receptors
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
    • Protein or peptide: Glutamate receptor 1
    • Protein or peptide: Isoform 2 of Glutamate receptor 4
  • Ligand: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
KeywordsiGluR / CP-AMPA receptors / MEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion ...Presynaptic depolarization and calcium channel opening / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion / response to sucrose / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / proximal dendrite / myosin V binding / neuron spine / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / channel regulator activity / cellular response to L-glutamate / regulation of AMPA receptor activity / regulation of monoatomic ion transmembrane transport / conditioned place preference / response to arsenic-containing substance / cellular response to dsRNA / membrane hyperpolarization / regulation of synapse structure or activity / dendritic spine membrane / Synaptic adhesion-like molecules / nervous system process / protein targeting to membrane / long-term synaptic depression / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / voltage-gated calcium channel complex / response to morphine / neuronal cell body membrane / peptide hormone receptor binding / protein kinase A binding / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / response to psychosocial stress / spinal cord development / Activation of AMPA receptors / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / : / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / behavioral response to pain / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / adenylate cyclase binding / membrane depolarization / asymmetric synapse / regulation of receptor recycling / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / long-term memory / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / response to electrical stimulus / neuronal action potential / glutamate-gated receptor activity / response to fungicide / synapse assembly / ionotropic glutamate receptor binding / presynaptic active zone membrane / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / calcium channel regulator activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / 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 / PDZ domain binding / cellular response to amino acid stimulus / response to cocaine / synaptic membrane / response to nutrient levels / modulation of chemical synaptic transmission / postsynaptic density membrane / : / terminal bouton / neuromuscular junction / cellular response to growth factor stimulus
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 1 / Glutamate receptor 4 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsFang CF / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: Gating and noelin clustering of native Ca2+-permeable AMPA receptors
Authors: Fang C / Spangler CJ / Park J / Sheldon N / Trussell LO / Gouaux E
History
DepositionMar 14, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49726.png

Downloads & links

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Map

FileDownload / File: emd_49726.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 224 pix.
= 421.12 Å		1.88 Å/pix.
x 224 pix.
= 421.12 Å		1.88 Å/pix.
x 224 pix.
= 421.12 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.664
Minimum - Maximum-2.4107897 - 3.7758145
Average (Standard dev.)0.0010021611 (±0.07162531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 421.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49726_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49726_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49726_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CP-AMPA receptors

EntireName: CP-AMPA receptors
Components
  • Complex: CP-AMPA receptors
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
    • Protein or peptide: Glutamate receptor 1
    • Protein or peptide: Isoform 2 of Glutamate receptor 4
  • Ligand: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid

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Supramolecule #1: CP-AMPA receptors

SupramoleculeName: CP-AMPA receptors / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Voltage-dependent calcium channel gamma-2 subunit

MacromoleculeName: 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: 22.589975 KDa
SequenceString: DRGVQMLLTT VGAFAAFSLM TIAVGTDYWL YSRGVCKTKS VSENETSKKN EEVMTHSGLW RTCCLEGNFK GLCKQIDHFP EDADYEADT AEYFLRAVRA SSIFPILSVI LLFMGGLCIA ASEFYKTRHN IILSAGIFFV SAGLSNIIGI IVYISANAGD P SKSDSKKN ...String:
DRGVQMLLTT VGAFAAFSLM TIAVGTDYWL YSRGVCKTKS VSENETSKKN EEVMTHSGLW RTCCLEGNFK GLCKQIDHFP EDADYEADT AEYFLRAVRA SSIFPILSVI LLFMGGLCIA ASEFYKTRHN IILSAGIFFV SAGLSNIIGI IVYISANAGD P SKSDSKKN SYSYGWSFYF GALSFIIAEM VGVLAVHMFI DRHKQL

UniProtKB: Voltage-dependent calcium channel gamma-2 subunit

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Macromolecule #2: Glutamate receptor 1

MacromoleculeName: Glutamate receptor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 47.879855 KDa
SequenceString: RTYIVTTILE DPYVMLKKNA NQFEGNDRYE GYCVELAAEI AKHVGYSYRL EIVSDGKYGA RDPDTKAWNG MVGELVYGRA DVAVAPLTI TLVREEVIDF SKPFMSLGIS IMIKKPQKSK PGVFSFLDPL AYEIWMCIVF AYIGVSVVLF LVSRFSPYEW H SEEFEEGR ...String:
RTYIVTTILE DPYVMLKKNA NQFEGNDRYE GYCVELAAEI AKHVGYSYRL EIVSDGKYGA RDPDTKAWNG MVGELVYGRA DVAVAPLTI TLVREEVIDF SKPFMSLGIS IMIKKPQKSK PGVFSFLDPL AYEIWMCIVF AYIGVSVVLF LVSRFSPYEW H SEEFEEGR DQTTSDQSNE FGIFNSLWFS LGAFMQQGCD ISPRSLSGRI VGGVWWFFTL IIISSYTANL AAFLTVERMV SP IESAEDL AKQTEIAYGT LEAGSTKEFF RRSKIAVFEK MWTYMKSAEP SVFVRTTEEG MIRVRKSKGK YAYLLESTMN EYI EQRKPC DTMKVGGNLD SKGYGIATPK GSALRNPVNL AVLKLNEQGL LDKLKNKWWY DKGECGSGGG DSKDKTSALS LSNV AGVFY ILIGGLGLAM LVALIEFCYK SR

UniProtKB: Glutamate receptor 1

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Macromolecule #3: Isoform 2 of Glutamate receptor 4

MacromoleculeName: Isoform 2 of Glutamate receptor 4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 47.173348 KDa
SequenceString: VVVTTIMESP YVMYKKNHEM FEGNDKYEGY CVDLASEIAK HIGIKYKIAI VPDGKYGARD ADTKIWNGMV GELVYGKAEI AIAPLTITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVVLFLV SRFSPYEWHT E EPEDGKEG ...String:
VVVTTIMESP YVMYKKNHEM FEGNDKYEGY CVDLASEIAK HIGIKYKIAI VPDGKYGARD ADTKIWNGMV GELVYGKAEI AIAPLTITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVVLFLV SRFSPYEWHT E EPEDGKEG PSDQPPNEFG IFNSLWFSLG AFMQQGCDIS PRSLSGRIVG GVWWFFTLII ISSYTANLAA FLTVERMVSP IE SAEDLAK QTEIAYGTLD SGSTKEFFRR SKIAVYEKMW TYMRSAEPSV FTRTTAEGVA RVRKSKGKFA FLLESTMNEY TEQ RKPCDT MKVGGNLDSK GYGVATPKGS SLRTPVNLAV LKLSEAGVLD KLKNKWWYDK GECGPKDSGS KDKTSALSLS NVAG VFYIL VGGLGLAMLV ALIEFCYKS

UniProtKB: Glutamate receptor 4

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Macromolecule #4: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquino...

MacromoleculeName: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
type: ligand / ID: 4 / Number of copies: 4 / Formula: ZK1
Molecular weightTheoretical: 409.254 Da
Chemical component information

ChemComp-ZK1:
{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / antagonist, medication*YM

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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

Concentration0.1 mg/mL
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.2 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: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 27128
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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