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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 / homologyGSG1-like / Ligand-gated ion channel / Ionotropic glutamate receptor, metazoa / Receptor, ligand binding region / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Periplasmic binding protein-like I / Ionotropic glutamate receptor / Receptor family ligand binding region / GSG1-like protein / Ligated ion channel L-glutamate- and glycine-binding site ...GSG1-like / Ligand-gated ion channel / Ionotropic glutamate receptor, metazoa / Receptor, ligand binding region / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Periplasmic binding protein-like I / Ionotropic glutamate receptor / Receptor family ligand binding region / GSG1-like protein / Ligated ion channel L-glutamate- and glycine-binding site / regulation of AMPA receptor activity / regulation of postsynaptic neurotransmitter receptor activity / AMPA glutamate receptor activity / asymmetric synapse / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / response to lithium ion / regulation of receptor recycling / positive regulation of synaptic transmission / SNARE binding / response to fungicide / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor activity / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / dendritic shaft / receptor internalization / synaptic vesicle membrane / dendrite cytoplasm / presynaptic membrane / PDZ domain binding / terminal bouton / chemical synaptic transmission / establishment of protein localization / protein tetramerization / signaling receptor activity / growth cone / amyloid-beta binding / postsynaptic membrane / ATPase binding / perikaryon / dendritic spine / postsynaptic density / synapse / cell junction / dendrite / neuronal cell body / endoplasmic reticulum membrane / protein kinase binding / integral component of plasma membrane / cell surface / protein-containing complex / integral component of membrane / identical protein binding / plasma membrane / Germ cell-specific gene 1-like protein / Glutamate receptor 2
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.6 Å resolution
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
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)707,34914
Polyers704,8276
Non-polymers2,5228
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)32740
ΔGint (kcal/M)-271
Surface area (Å2)162010

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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 (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


Mass: 409.254 Da / Num. of mol.: 4 / Formula: C14H15F3N3O6P
#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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 / 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: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 42637 / Symmetry type: POINT

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