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- PDB-9rnh: GluA4 in complex with TARP-2, Resting II state, structure of TMD ... -

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Basic information

Entry
Database: PDB / ID: 9rnh
TitleGluA4 in complex with TARP-2, Resting II state, structure of TMD domain
Components
  • Glutamate receptor
  • Voltage-dependent calcium channel gamma-2 subunit
KeywordsMEMBRANE PROTEIN / Gria4 / Voltage-dependent calcium channel gamma-2 / AMPA Receptor / GluA4-TARP2 / 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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / Glutamate receptor / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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
DepositionJun 19, 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

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor
B: Glutamate receptor
C: Glutamate receptor
D: Glutamate receptor
E: Voltage-dependent calcium channel gamma-2 subunit
F: Voltage-dependent calcium channel gamma-2 subunit
G: Voltage-dependent calcium channel gamma-2 subunit
H: Voltage-dependent calcium channel gamma-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)549,83414
Polymers547,8958
Non-polymers1,9396
Water181
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
Glutamate receptor


Mass: 101022.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria4 / Plasmid: pBICMam
Cell line (production host): Human embryonic kidney 293 cells
Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: A0A0G2JU28
#2: Protein
Voltage-dependent calcium channel gamma-2 subunit / Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin / Transmembrane AMPAR regulatory ...Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin / Transmembrane AMPAR regulatory protein gamma-2 / TARP gamma-2


Mass: 35950.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacng2, Stg / Plasmid: pBICMam
Cell line (production host): Human embryonic kidney 293 cells
Production host: Homo sapiens (human) / References: UniProt: Q71RJ2
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 II state, structure of TMD domain
Type: COMPLEX / Entity ID: #1-#2 / 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(hydroxymethyl)aminomethaneNH2C(CH2OH)31
30.02 %Glyco-diosgenin (GDN)C56H92O251
SpecimenConc.: 3.1 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 software
IDNameVersionCategory
1RELION5particle selection
12cryoSPARC4.3.13D reconstruction
13PHENIX1.19.2_4158:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105118 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310353
ELECTRON MICROSCOPYf_angle_d0.51213999
ELECTRON MICROSCOPYf_dihedral_angle_d6.4191483
ELECTRON MICROSCOPYf_chiral_restr0.0381589
ELECTRON MICROSCOPYf_plane_restr0.011685

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