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- PDB-9nra: The structure of GluA1/A4 LBD-TMD with 4 auxiliary subunits -

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Basic information

Entry
Database: PDB / ID: 9nra
TitleThe structure of GluA1/A4 LBD-TMD with 4 auxiliary subunits
Components
  • Auxiliary protein at A'/C'
  • Glutamate receptor 1
  • Isoform 2 of Glutamate receptor 4
  • Voltage-dependent calcium channel gamma-2 subunit
KeywordsMEMBRANE PROTEIN / iGluR / CP-AMPA receptors
Function / homology
Function and homology information


Cargo concentration in the ER / Presynaptic depolarization and calcium channel opening / axonal spine / positive regulation of locomotion involved in locomotory behavior / COPII-mediated vesicle transport / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion / response to sucrose ...Cargo concentration in the ER / Presynaptic depolarization and calcium channel opening / axonal spine / positive regulation of locomotion involved in locomotory behavior / COPII-mediated vesicle transport / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion / response to sucrose / myosin V binding / cerebellar mossy fiber / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / postsynaptic neurotransmitter receptor diffusion trapping / proximal dendrite / regulation of AMPA receptor activity / kainate selective glutamate receptor complex / response to arsenic-containing substance / regulation of monoatomic ion transmembrane transport / channel regulator activity / cellular response to L-glutamate / membrane hyperpolarization / ligand-gated calcium channel activity / regulation of synapse structure or activity / cellular response to dsRNA / dendritic spine membrane / nervous system process / beta-2 adrenergic receptor binding / Synaptic adhesion-like molecules / long-term synaptic depression / protein targeting to membrane / cellular response to peptide hormone stimulus / voltage-gated calcium channel complex / cellular response to amine stimulus / peptide hormone receptor binding / response to psychosocial stress / Activation of AMPA receptors / neurotransmitter receptor localization to postsynaptic specialization membrane / response to morphine / perisynaptic space / spinal cord development / neuronal cell body membrane / protein kinase A binding / neuromuscular junction development / Trafficking of GluR2-containing AMPA receptors / negative regulation of smooth muscle cell apoptotic process / response to lithium ion / AMPA glutamate receptor activity / transmission of nerve impulse / immunoglobulin binding / adenylate cyclase binding / behavioral response to pain / asymmetric synapse / AMPA glutamate receptor complex / regulation of receptor recycling / response to electrical stimulus / cellular response to glycine / membrane depolarization / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / conditioned place preference / glutamate receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / long-term memory / postsynaptic density, intracellular component / response to fungicide / neuronal action potential / positive regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / glutamate-gated calcium ion channel activity / synapse assembly / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / dendritic shaft / synaptic membrane / calcium channel regulator activity / PDZ domain binding / response to cocaine / neuromuscular junction / cellular response to amino acid stimulus / synaptic transmission, glutamatergic / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to nutrient levels / cerebral cortex development / receptor internalization / regulation of synaptic plasticity / response to calcium ion
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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site ...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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / 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
Chem-ZK1 / Glutamate receptor 1 / Glutamate receptor 4 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsFang, C.L. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: Gating and noelin clustering of native Ca-permeable AMPA receptors.
Authors: Chengli Fang / Cathy J Spangler / Jumi Park / Natalie Sheldon / Laurence O Trussell / Eric Gouaux /
Abstract: AMPA-type ionotropic glutamate receptors (AMPARs) are integral to fast excitatory synaptic transmission and have vital roles in synaptic plasticity, motor coordination, learning and memory. Whereas ...AMPA-type ionotropic glutamate receptors (AMPARs) are integral to fast excitatory synaptic transmission and have vital roles in synaptic plasticity, motor coordination, learning and memory. Whereas extensive structural studies have been conducted on recombinant AMPARs and native calcium-impermeable (CI)-AMPARs alongside their auxiliary proteins, the molecular architecture of native calcium-permeable (CP)-AMPARs has remained undefined. Here, to determine the subunit composition, physiological architecture and gating mechanisms of CP-AMPARs, we visualize these receptors, immunoaffinity purified from rat cerebella, and resolve their structures using cryo-electron microscopy (cryo-EM). Our results indicate that the predominant assembly consists of GluA1 and GluA4 subunits, with the GluA4 subunit occupying the B and D positions, and auxiliary subunits, including transmembrane AMPAR regulatory proteins (TARPs) located at the B' and D' positions, and cornichon homologues (CNIHs) or TARPs located at the A' and C' positions. Furthermore, we resolved the structure of the noelin (NOE1)-GluA1-GluA4 complex, in which NOE1 specifically binds to the GluA4 subunit at the B and D positions. Notably, NOE1 stabilizes the amino-terminal domain layer without affecting gating properties of the receptor. NOE1 contributes to AMPAR function by forming dimeric AMPAR assemblies that are likely to engage in extracellular networks, clustering receptors in synaptic environments and modulating receptor responsiveness to synaptic inputs.
History
DepositionMar 14, 2025Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 1
B: Isoform 2 of Glutamate receptor 4
C: Glutamate receptor 1
D: Isoform 2 of Glutamate receptor 4
E: Auxiliary protein at A'/C'
F: Voltage-dependent calcium channel gamma-2 subunit
G: Auxiliary protein at A'/C'
H: Voltage-dependent calcium channel gamma-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,89812
Polymers255,2618
Non-polymers1,6374
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 Glutamate receptor 1 / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / AMPA 1


Mass: 47879.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P19490
#2: Protein Isoform 2 of Glutamate receptor 4 / GluR-4 / GluR4 / AMPA-selective glutamate receptor 4 / GluR-D / Glutamate receptor ionotropic / AMPA 4 / GluA4


Mass: 47185.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P19493
#3: Protein Auxiliary protein at A'/C'


Mass: 9975.288 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
#4: Protein Voltage-dependent calcium channel gamma-2 subunit


Mass: 22589.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q71RJ2
#5: Chemical
ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Comment: antagonist, medication*YM
Has ligand of interestN
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: CP-AMPA receptors / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14278 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315957
ELECTRON MICROSCOPYf_angle_d0.82421800
ELECTRON MICROSCOPYf_dihedral_angle_d5.2892337
ELECTRON MICROSCOPYf_chiral_restr0.0462579
ELECTRON MICROSCOPYf_plane_restr0.0052729

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