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- EMDB-54092: GluA4 in complex with TARP-2, Resting II state, structure of TMD ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54092
TitleGluA4 in complex with TARP-2, Resting II state, structure of TMD domain
Map data
Sample
  • Complex: GluA4 in complex with TARP-2, Resting II state, structure of TMD domain
    • Protein or peptide: Glutamate receptor
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
  • Ligand: PALMITIC ACID
  • Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: water
KeywordsGria4 / Voltage-dependent calcium channel gamma-2 / AMPA Receptor / GluA4-TARP2 / Membrane protein / Resting state II / TMD
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 / protein targeting to membrane / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / AMPA glutamate receptor activity / transmission of nerve impulse / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / membrane depolarization / positive regulation of synaptic transmission, glutamatergic / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / 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 / calcium channel regulator activity / response to calcium ion / postsynaptic density membrane / Schaffer collateral - CA1 synapse / postsynaptic membrane / glutamatergic synapse / cell surface
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 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus novergicus (Norway rat) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVega-Gutierrez C / Herguedas B
Funding support Spain, 1 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-106284GA-I00 Spain
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: GluA4 AMPA receptor gating mechanisms and modulation by auxiliary subunits
Authors: Vega-Gutierrez C / Herguedas B / Soto D / Sanchez-Valls I / Picanol-Parraga J
History
DepositionJun 19, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54092.png

Downloads & links

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Map

FileDownload / File: emd_54092.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 496 pix.
= 320.515 Å		0.65 Å/pix.
x 496 pix.
= 320.515 Å		0.65 Å/pix.
x 496 pix.
= 320.515 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6462 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.421
Minimum - Maximum-1.4235514 - 2.38311
Average (Standard dev.)0.001514443 (±0.063682795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions496496496
Spacing496496496
CellA=B=C: 320.5152 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54092_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54092_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_54092_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : GluA4 in complex with TARP-2, Resting II state, structure of TMD ...

EntireName: GluA4 in complex with TARP-2, Resting II state, structure of TMD domain
Components
  • Complex: GluA4 in complex with TARP-2, Resting II state, structure of TMD domain
    • Protein or peptide: Glutamate receptor
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
  • Ligand: PALMITIC ACID
  • Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: water

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Supramolecule #1: GluA4 in complex with TARP-2, Resting II state, structure of TMD ...

SupramoleculeName: GluA4 in complex with TARP-2, Resting II state, structure of TMD domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus novergicus (Norway rat)
Molecular weightTheoretical: 620 KDa

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Macromolecule #1: Glutamate receptor

MacromoleculeName: Glutamate receptor / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 101.022945 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRIICRQIVL LFSGFWGLAM GAFPSSVQIG GLFIRNTDQE YTAFRLAIFL HNTSPNASEA PFNLVPHVDN IETANSFAVT NAFCSQYSR GVFAIFGLYD KRSVHTLTSF CSALHISLIT PSFPTEGESQ FVLQLRPSLR GALLSLLDHY EWNCFVFLYD T DRGYSILQ ...String:
MRIICRQIVL LFSGFWGLAM GAFPSSVQIG GLFIRNTDQE YTAFRLAIFL HNTSPNASEA PFNLVPHVDN IETANSFAVT NAFCSQYSR GVFAIFGLYD KRSVHTLTSF CSALHISLIT PSFPTEGESQ FVLQLRPSLR GALLSLLDHY EWNCFVFLYD T DRGYSILQ AIMEKAGQNG WHVSAICVEN FNDVSYRQLL EELDRRQEKK FVIDCEIERL QNILEQIVSV GKHVKGYHYI IA NLGFKDI SLERFIHGGA NVTGFQLVDF NTPMVTKLMD RWKKLDQREY PGSETPPKYT SALTYDGVLV MAETFRSLRR QKI DISRRG NAGDCLANPA APWGQGIDME RTLKQVRIQG LTGNVQFDHY GRRVNYTMDV FELKSTGPRK VGYWNDMDKL VLIQ DMPTL GNDTAAIENR TVVVTTIMES PYVMYKKNHE MFEGNDKYEG YCVDLASEIA KHIGIKYKIA IVPDGKYGAR DADTK IWNG MVGELVYGKA EIAIAPLTIT LVREEVIDFS KPFMSLGISI MIKKPQKSKP GVFSFLDPLA YEIWMCIVFA YIGVSV VLF LVSRFSPYEW HTEEPEDGKE GPSDQPPNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTA NL AAFLTVERMV SPIESAEDLA KQTEIAYGTL DSGSTKEFFR RSKIAVYEKM WTYMRSAEPS VFTRTTAEGV ARVRKSKG K FAFLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGVATPKG SSLRTPVNLA VLKLSEAGVL DKLKNKWWYD KGECGPKDS GSKDKTSALS LSNVAGVFYI LVGGLGLAML VALIEFCYKS RAEAKRMKLT FSEAIRNKAR LSITGSVGEN GRVLTPDCPK AVHTGTAIR QSSGLAVIAS DLP

UniProtKB: Glutamate receptor

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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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 35.950801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGLFDRGVQM LLTIVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD ...String:
MGLFDRGVQM LLTIVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD SKKNSYSYGW SFYFGALSFI IAEMVGVLAV HMFIDRHKQL RATARATDYL QASAITRIPS YRYRYQRRSR SS SRSTEPS HSRDASPVGV KGFNTLPSTE ISMYTLSRDP LKAATTPTAT YNSDRDNSFL QVHNCIQKDS KDSLHANTAN RRT TPV

UniProtKB: Voltage-dependent calcium channel gamma-2 subunit

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Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #4: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

MacromoleculeName: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / type: ligand / ID: 4 / Number of copies: 4 / Formula: OLC
Molecular weightTheoretical: 356.54 Da
Chemical component information

ChemComp-OLC:
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMNH2C(CH2OH)3Tris(hydroxymethyl)aminomethane
0.02 %C56H92O25Glyco-diosgenin (GDN)
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was incubated with the AMPA receptor antagonist (NBQX) to capture the receptor in its resting state

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 56948 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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
Details: An Ab-initio Reconstruction was generated in CryoSPARC 4.3.1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 105118
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationDetails: 3D classification without alignment
FSC plot (resolution estimation)

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