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- PDB-5vhz: GluA2-2xGSG1L bound to L-Quisqualate -

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Entry
Database: PDB / ID: 5vhz
TitleGluA2-2xGSG1L bound to L-Quisqualate
ComponentsGlutamate receptor 2,Germ cell-specific gene 1-like protein
KeywordsTRANSPORT PROTEIN / Ion channel
Function/homologyGSG1-like / regulation of postsynaptic neurotransmitter receptor activity / GSG1-like protein / regulation of AMPA receptor activity / regulation of molecular function / asymmetric synapse / AMPA glutamate receptor activity / integral component of postsynaptic density membrane / AMPA glutamate receptor complex / kainate selective glutamate receptor activity ...GSG1-like / regulation of postsynaptic neurotransmitter receptor activity / GSG1-like protein / regulation of AMPA receptor activity / regulation of molecular function / asymmetric synapse / AMPA glutamate receptor activity / integral component of postsynaptic density membrane / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / postsynaptic density membrane / ionotropic glutamate receptor complex / somatodendritic compartment / response to lithium ion / regulation of synaptic transmission, glutamatergic / regulation of receptor recycling / positive regulation of synaptic transmission / synaptic membrane / SNARE binding / response to fungicide / synaptic vesicle membrane / Ionotropic glutamate receptor, metazoa / ionotropic glutamate receptor activity / extracellularly glutamate-gated ion channel activity / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / ionotropic glutamate receptor signaling pathway / Ligand-gated ion channel / Ionotropic glutamate receptor / Receptor, ligand binding region / dendritic shaft / Ligated ion channel L-glutamate- and glycine-binding site / cytoskeletal protein binding / dendrite cytoplasm / PDZ domain binding / presynaptic membrane / receptor internalization / synaptic vesicle / Receptor family ligand binding region / terminal bouton / Periplasmic binding protein-like I / growth cone / establishment of protein localization / chemical synaptic transmission / protein tetramerization / postsynaptic membrane / go:0004872: / amyloid-beta binding / ATPase binding / perikaryon / dendritic spine / postsynaptic density / synapse / neuron projection / cell junction / neuronal cell body / dendrite / endoplasmic reticulum membrane / protein kinase binding / integral component of plasma membrane / endoplasmic reticulum / cell surface / go:0043234: / membrane / identical protein binding / Germ cell-specific gene 1-like protein / Glutamate receptor 2
Function and homology information
Specimen sourceRattus norvegicus / Brown rat / mammal /
MethodElectron microscopy (8.4 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsTwomey, E.C. / Yelshanskaya, M.V. / Grassucci, R.A. / Frank, J. / Sobolevsky, A.I.
CitationJournal: Neuron / Year: 2017
Title: Structural Bases of Desensitization in AMPA Receptor-Auxiliary Subunit Complexes.
Authors: Edward C Twomey / Maria V Yelshanskaya / Robert A Grassucci / Joachim Frank / Alexander I Sobolevsky
Abstract: Fast excitatory neurotransmission is mediated by AMPA-subtype ionotropic glutamate receptors (AMPARs). AMPARs, localized at post-synaptic densities, are regulated by transmembrane auxiliary subunits ...Fast excitatory neurotransmission is mediated by AMPA-subtype ionotropic glutamate receptors (AMPARs). AMPARs, localized at post-synaptic densities, are regulated by transmembrane auxiliary subunits that modulate AMPAR assembly, trafficking, gating, and pharmacology. Aberrancies in AMPAR-mediated signaling are associated with numerous neurological disorders. Here, we report cryo-EM structures of an AMPAR in complex with the auxiliary subunit GSG1L in the closed and desensitized states. GSG1L favors the AMPAR desensitized state, where channel closure is facilitated by profound structural rearrangements in the AMPAR extracellular domain, with ligand-binding domain dimers losing their local 2-fold rotational symmetry. Our structural and functional experiments suggest that AMPAR auxiliary subunits share a modular architecture and use a common transmembrane scaffold for distinct extracellular modules to differentially regulate AMPAR gating. By comparing the AMPAR-GSG1L complex structures, we map conformational changes accompanying AMPAR recovery from desensitization and reveal structural bases for regulation of synaptic transmission by auxiliary subunits.
Copyright: 2017 Elsevier Inc. All rights reserved.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2017 / Release: May 3, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 3, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelDatabase references
1.2Nov 8, 2017Structure modelData collection / Derived calculations / Experimental preparationem_image_scans / em_sample_support / pdbx_struct_assembly_em_sample_support.grid_type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

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Assembly

Deposited unit
A: Glutamate receptor 2,Germ cell-specific gene 1-like protein
B: Glutamate receptor 2,Germ cell-specific gene 1-like protein
C: Glutamate receptor 2,Germ cell-specific gene 1-like protein
D: Glutamate receptor 2,Germ cell-specific gene 1-like protein
E: Glutamate receptor 2,Germ cell-specific gene 1-like protein
F: Glutamate receptor 2,Germ cell-specific gene 1-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)705,58410
Polyers704,8276
Non-polymers7574
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)30010
ΔGint (kcal/M)-288
Surface area (Å2)159720

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Components

#1: Protein/peptide
Glutamate receptor 2,Germ cell-specific gene 1-like protein / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / GSG1-like protein


Mass: 117471.211 Da / Num. of mol.: 6
Source: (gene. exp.) Rattus norvegicus / Brown rat / mammal /
Gene: Gria2, Glur2, Gsg1l / Cell line (production host): HEK-293S / Production host: Homo sapiens / References: UniProt:P19491, UniProt:D3ZK93
#2: Chemical
ChemComp-QUS / (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID / QUISQUALATE


Mass: 189.126 Da / Num. of mol.: 4 / Formula: C5H7N3O5 / : Quisqualic acid

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: GluA2-2xGSG1L bound to L-Quisqualate cryo-EM density / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus
Source (recombinant)Organism: Rattus norvegicus
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Details: GluA2-2xGSG1L bound to L-Quisqualate / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Gold-gold grids, hydrogen and oxygen glow discharge (20s, 10 watts, 6.4 sccm H2, 27.5 sccm O2)
Grid material: GOLD / Grid mesh size: 200 / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 67 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 51130 / Symmetry type: POINT

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