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- PDB-5vhy: GluA2-2xGSG1L bound to ZK -

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Basic information

Entry
Database: PDB / ID: 5vhy
TitleGluA2-2xGSG1L bound to ZK
ComponentsGlutamate receptor 2,Germ cell-specific gene 1-like protein
KeywordsTRANSPORT PROTEIN / Ion channel
Function / homology
Function and homology information


regulation of postsynaptic neurotransmitter receptor activity / regulation of AMPA receptor activity / regulation of postsynaptic neurotransmitter receptor internalization / AMPA glutamate receptor activity / asymmetric synapse / extracellularly glutamate-gated ion channel activity / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / response to lithium ion ...regulation of postsynaptic neurotransmitter receptor activity / regulation of AMPA receptor activity / regulation of postsynaptic neurotransmitter receptor internalization / AMPA glutamate receptor activity / asymmetric synapse / extracellularly glutamate-gated ion channel activity / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / response to lithium ion / regulation of receptor recycling / immunoglobulin binding / somatodendritic compartment / positive regulation of synaptic transmission / integral component of postsynaptic membrane / ionotropic glutamate receptor activity / SNARE binding / response to fungicide / regulation of synaptic transmission, glutamatergic / integral component of postsynaptic density membrane / synaptic membrane / glutamate receptor activity / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / synaptic vesicle membrane / ionotropic glutamate receptor signaling pathway / synaptic transmission, glutamatergic / cytoskeletal protein binding / dendritic shaft / postsynaptic density membrane / dendrite cytoplasm / integral component of presynaptic membrane / PDZ domain binding / receptor internalization / Schaffer collateral - CA1 synapse / presynaptic membrane / protein tetramerization / terminal bouton / establishment of protein localization / modulation of chemical synaptic transmission / growth cone / postsynaptic membrane / chemical synaptic transmission / synaptic vesicle / amyloid-beta binding / ATPase binding / perikaryon / signaling receptor activity / dendritic spine / postsynaptic density / neuron projection / synapse / cell junction / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / neuronal cell body / protein kinase binding / endoplasmic reticulum / integral component of plasma membrane / cell surface / protein-containing complex / membrane / identical protein binding / plasma membrane
Ligated ion channel L-glutamate- and glycine-binding site / GSG1-like protein / Ionotropic glutamate receptor / Receptor, ligand binding region / GSG1-like / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Periplasmic binding protein-like I / Ionotropic glutamate receptor, metazoa / Ligand-gated ion channel / Receptor family ligand binding region
Germ cell-specific gene 1-like protein / Glutamate receptor 2
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Nov 8, 2017Group: Data collection / Derived calculations / Experimental preparation
Category: em_image_scans / em_sample_support / pdbx_struct_assembly
Item: _em_sample_support.grid_type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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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)707,34914
Polymers704,8276
Non-polymers2,5228
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area32740 Å2
ΔGint-271 kcal/mol
Surface area162010 Å2

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Components

#1: Protein
Glutamate receptor 2,Germ cell-specific gene 1-like protein / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2, Gsg1l / Cell line (production host): HEK-293S / Production host: Homo sapiens (human) / References: UniProt: P19491, UniProt: D3ZK93
#2: 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 / Fanapanel


Mass: 409.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Comment: antagonist, medication*YM
#3: Sugar
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6

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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: GluA2-2xGSG1L ZK cryo-EM density / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / 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 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 80 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 (2 fold cyclic)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42637 / Symmetry type: POINT

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