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- EMDB-8820: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-8820
TitleGluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Map data
SampleGluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
  • Chimera of Glutamate receptor 2, Germ cell-specific gene 1-like protein
  • (ligand) x 2
Function / homology
Function and homology information


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 ...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
Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / GSG1-like / Receptor, ligand binding region / Ionotropic glutamate receptor / Ionotropic glutamate receptor, metazoa
Germ cell-specific gene 1-like protein / Glutamate receptor 2
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsTwomey EC / Yelshanskaya MV / Grassucci RA / Frank J / Sobolevsky AI
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS093838 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206573 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083660 United States
Howard Hughes Medical Institute (HHMI)GM029169 United States
CitationJournal: Nature / Year: 2017
Title: Channel opening and gating mechanism in AMPA-subtype glutamate receptors.
Authors: Edward C Twomey / Maria V Yelshanskaya / Robert A Grassucci / Joachim Frank / Alexander I Sobolevsky /
Abstract: AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid)-subtype ionotropic glutamate receptors mediate fast excitatory neurotransmission throughout the central nervous system. Gated by the ...AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid)-subtype ionotropic glutamate receptors mediate fast excitatory neurotransmission throughout the central nervous system. Gated by the neurotransmitter glutamate, AMPA receptors are critical for synaptic strength, and dysregulation of AMPA receptor-mediated signalling is linked to numerous neurological diseases. Here we use cryo-electron microscopy to solve the structures of AMPA receptor-auxiliary subunit complexes in the apo, antagonist- and agonist-bound states and determine the iris-like mechanism of ion channel opening. The ion channel selectivity filter is formed by the extended portions of the re-entrant M2 loops, while the helical portions of M2 contribute to extensive hydrophobic interfaces between AMPA receptor subunits in the ion channel. We show how the permeation pathway changes upon channel opening and identify conformational changes throughout the entire AMPA receptor that accompany activation and desensitization. Our findings provide a framework for understanding gating across the family of ionotropic glutamate receptors and the role of AMPA receptors in excitatory neurotransmission.
Validation ReportPDB-ID: 5wel

SummaryFull reportAbout validation report
History
DepositionJul 10, 2017-
Header (metadata) releaseAug 2, 2017-
Map releaseAug 2, 2017-
UpdateNov 20, 2019-
Current statusNov 20, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5wel
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8820.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 300 pix.
= 294. Å
0.98 Å/pix.
x 300 pix.
= 294. Å
0.98 Å/pix.
x 300 pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.06896673 - 0.13429308
Average (Standard dev.)0.000805433 (±0.0049637896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0690.1340.001

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Supplemental data

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Sample components

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Entire GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2

EntireName: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Number of components: 4

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Component #1: protein, GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2

ProteinName: GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Chimera of Glutamate receptor 2, Germ cell-specific gene...

ProteinName: Chimera of Glutamate receptor 2, Germ cell-specific gene 1-like protein
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 117.471211 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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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, Digitonin

LigandName: Digitonin / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.229312 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: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 67 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 41926
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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