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- PDB-9igz: GluA4 in complex with TARP-2, resting state, structure of N-termi... -

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Basic information

Entry
Database: PDB / ID: 9igz
TitleGluA4 in complex with TARP-2, resting state, structure of N-terminal domain
ComponentsIsoform 2 of Glutamate receptor 4
KeywordsMEMBRANE PROTEIN / Gria4 / Voltage-dependent calcium channel gamma-2 / AMPA Receptor / GluA4-TARP2 / Resting state / NTD
Function / homology
Function and homology information


Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission, glutamatergic / response to fungicide / glutamate-gated receptor activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / chemical synaptic transmission / dendritic spine / postsynaptic density / neuronal cell body / dendrite / synapse / glutamatergic synapse / identical protein binding / plasma membrane
Similarity search - Function
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 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsVega-Gutierrez, C. / Herguedas, B.
Funding support Spain, 1items
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 proteins.
Authors: Carlos Vega-Gutiérrez / Javier Picañol-Párraga / Irene Sánchez-Valls / Victoria Del Pilar Ribón-Fuster / David Soto / Beatriz Herguedas /
Abstract: AMPA-type glutamate receptors, fundamental ion channels for fast excitatory neurotransmission and synaptic plasticity, contain a GluA tetrameric core surrounded by auxiliary proteins such as ...AMPA-type glutamate receptors, fundamental ion channels for fast excitatory neurotransmission and synaptic plasticity, contain a GluA tetrameric core surrounded by auxiliary proteins such as transmembrane AMPA receptor regulatory proteins (TARPs) or Cornichons. Their exact composition and stoichiometry govern functional properties, including kinetics, calcium permeability and trafficking. The GluA1-GluA3 subunits predominate in the adult forebrain and are well characterized. However, we lack structural information on full-length GluA4-containing AMPARs, a subtype that has specific roles in brain development and specific cell types in mammals. Here we present the cryo-electron microscopy structures of rat GluA4:TARP-γ2 trapped in active, resting and desensitized states, covering a full gating cycle. Additionally, we describe the structure of GluA4 alone, which displays a classical Y-shaped conformation. In resting conditions, GluA4:TARP-γ2 adopts two conformations, one resembling the desensitized states of other GluA subunits. Moreover, we identify a regulatory site for TARP-γ2 in the ligand-binding domain that modulates gating kinetics. Our findings uncover distinct features of GluA4, highlighting how subunit composition and auxiliary proteins shape receptor structure and dynamics, expanding glutamatergic signaling diversity.
History
DepositionFeb 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Isoform 2 of Glutamate receptor 4
C: Isoform 2 of Glutamate receptor 4
B: Isoform 2 of Glutamate receptor 4
A: Isoform 2 of Glutamate receptor 4


Theoretical massNumber of molelcules
Total (without water)394,6884
Polymers394,6884
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Isoform 2 of Glutamate receptor 4 / GluR-4 / GluR4 / AMPA-selective glutamate receptor 4 / GluR-D / Glutamate receptor ionotropic / AMPA 4 / GluA4


Mass: 98671.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria4, Glur4 / Plasmid: pBICMam
Cell line (production host): Human embryonic kidney 293 cells
Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P19493
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GluA4 in complex with TARP-2, resting state, structure of N-terminal domain
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.62 MDa / Experimental value: NO
Source (natural)Organism: Rattus novergicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pBICMam
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTris(hidroximetil)-aminometanoNH2C(CH2OH)31
30.02 %Glyco-diosgenin (GDN)C56H92O251
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was incubated with the AMPA receptor antagonist (NBQX) to capture the receptor in its resting state.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 56948

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88447 / Symmetry type: POINT
Atomic model buildingB value: 74.49 / Protocol: RIGID BODY FIT / Space: REAL
Details: Four monomers of GluA4 NTD (PDB: 4GPA) were rigid body fitted in Chimera followed by manual modelling in Coot and real space refinement in Phenix.
Atomic model buildingPDB-ID: 4GPA

4gpa


Pdb chain-ID: A / Accession code: 4GPA / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211936
ELECTRON MICROSCOPYf_angle_d0.39516180
ELECTRON MICROSCOPYf_dihedral_angle_d3.341600
ELECTRON MICROSCOPYf_chiral_restr0.0391804
ELECTRON MICROSCOPYf_plane_restr0.0042080

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