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- EMDB-8686: GluA2-1xGSG1L bound to ZK -

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Basic information

Entry
Database: EMDB / ID: 8686
TitleGluA2-1xGSG1L bound to ZK
Map dataGluA2-1xGSG1L bound to ZK
SampleGluA2-1xGSG1L cryo-EM density
  • Glutamate receptor 2,Germ cell-specific gene 1-like protein
  • (ligand) x 2
Function / homologyReceptor, ligand binding region / Receptor family ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / GSG1-like / Ligand-gated ion channel / Periplasmic binding protein-like I / Ligated ion channel L-glutamate- and glycine-binding site / GSG1-like protein ...Receptor, ligand binding region / Receptor family ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / GSG1-like / Ligand-gated ion channel / Periplasmic binding protein-like I / Ligated ion channel L-glutamate- and glycine-binding site / GSG1-like protein / regulation of postsynaptic neurotransmitter receptor activity / integral component of postsynaptic density membrane / regulation of AMPA receptor activity / AMPA glutamate receptor activity / asymmetric synapse / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / response to lithium ion / regulation of synaptic transmission, glutamatergic / regulation of receptor recycling / positive regulation of synaptic transmission / SNARE binding / response to fungicide / synaptic vesicle membrane / ionotropic glutamate receptor activity / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor signaling pathway / dendritic shaft / PDZ domain binding / presynaptic membrane / dendrite cytoplasm / receptor internalization / terminal bouton / chemical synaptic transmission / growth cone / establishment of protein localization / signaling receptor activity / protein tetramerization / amyloid-beta binding / postsynaptic membrane / ATPase binding / perikaryon / postsynaptic density / dendritic spine / synapse / cell junction / neuronal cell body / dendrite / endoplasmic reticulum membrane / integral component of plasma membrane / cell surface / protein-containing complex / identical protein binding / Germ cell-specific gene 1-like protein / Glutamate receptor 2
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 8.3 Å resolution
AuthorsTwomey EC / Yelshanskaya MV
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 ReportPDB-ID: 5vhx

SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Nov 8, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5vhx
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8686.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.04 Å/pix.
= 374.4 Å
360 pix
1.04 Å/pix.
= 374.4 Å
360 pix
1.04 Å/pix.
= 374.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:0.022 (by author), 0.022 (movie #1):
Minimum - Maximum-0.017233951 - 0.057763822
Average (Standard dev.)0.00044932571 (0.002892311)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z374.400374.400374.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0170.0580.000

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Supplemental data

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Sample components

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Entire GluA2-1xGSG1L cryo-EM density

EntireName: GluA2-1xGSG1L cryo-EM density / Number of components: 4

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Component #1: protein, GluA2-1xGSG1L cryo-EM density

ProteinName: GluA2-1xGSG1L cryo-EM density / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Rattus norvegicus (Norway rat)

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Component #2: protein, Glutamate receptor 2,Germ cell-specific gene 1-like protein

ProteinName: Glutamate receptor 2,Germ cell-specific gene 1-like protein
Recombinant expression: No
MassTheoretical: 117.471211 kDa
Source (engineered)Expression System: Rattus norvegicus (Norway rat)

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Component #3: ligand, {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihy...

LigandName: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.409254 kDa

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Component #4: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 8
Support filmGold-gold grids, hydrogen and oxygen glow discharge (20s, 10 watts, 6.4 sccm H2, 27.5 sccm O2)
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 80 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 16454
3D reconstructionResolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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