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- EMDB-8232: Cryo-EM structure of GluA2 bound to antagonist ZK200775 at 6.8 An... -

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Entry
Database: EMDB / ID: 8232
TitleCryo-EM structure of GluA2 bound to antagonist ZK200775 at 6.8 Angstrom resolution
Map dataCryo-EM structure of GluA2 bound to antagonist ZK200775 at 6.8 Angstrom resolution
SampleProtein:
Glutamate receptor 2GRIA2 / (ligand) x 2
Function / homologyIonotropic glutamate receptor / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Receptor family ligand binding region / Ligand-gated ion channel / Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Receptor, ligand binding region / AMPA glutamate receptor activity / asymmetric synapse ...Ionotropic glutamate receptor / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Receptor family ligand binding region / Ligand-gated ion channel / Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Receptor, ligand binding region / 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 receptor recycling / SNARE binding / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / positive regulation of synaptic transmission / integral component of postsynaptic membrane / regulation of synaptic transmission, glutamatergic / response to fungicide / integral component of postsynaptic density membrane / ionotropic glutamate receptor activity / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / synaptic vesicle membrane / dendritic shaft / dendrite cytoplasm / receptor internalization / integral component of presynaptic membrane / PDZ domain binding / Schaffer collateral - CA1 synapse / presynaptic membrane / terminal bouton / establishment of protein localization / protein tetramerization / growth cone / chemical synaptic transmission / amyloid-beta binding / ATPase binding / perikaryon / signaling receptor activity / dendritic spine / postsynaptic density / cell junction / synapse / glutamatergic synapse / dendrite / endoplasmic reticulum membrane / neuronal cell body / protein kinase binding / integral component of plasma membrane / cell surface / protein-containing complex / identical protein binding / plasma membrane / Glutamate receptor 2
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 6.8 Å resolution
AuthorsTwomey EC / Yelshanskaya MV / Grassucci RG / Frank J / Sobolevsky AI
CitationJournal: Science / Year: 2016
Title: Elucidation of AMPA receptor-stargazin complexes by cryo-electron microscopy.
Authors: Edward C Twomey / Maria V Yelshanskaya / Robert A Grassucci / Joachim Frank / Alexander I Sobolevsky
Abstract: AMPA-subtype ionotropic glutamate receptors (AMPARs) mediate fast excitatory neurotransmission and contribute to high cognitive processes such as learning and memory. In the brain, AMPAR trafficking, ...AMPA-subtype ionotropic glutamate receptors (AMPARs) mediate fast excitatory neurotransmission and contribute to high cognitive processes such as learning and memory. In the brain, AMPAR trafficking, gating, and pharmacology is tightly controlled by transmembrane AMPAR regulatory proteins (TARPs). Here, we used cryo-electron microscopy to elucidate the structural basis of AMPAR regulation by one of these auxiliary proteins, TARP γ2, or stargazin (STZ). Our structures illuminate the variable interaction stoichiometry of the AMPAR-TARP complex, with one or two TARP molecules binding one tetrameric AMPAR. Analysis of the AMPAR-STZ binding interfaces suggests that electrostatic interactions between the extracellular domains of AMPAR and STZ play an important role in modulating AMPAR function through contact surfaces that are conserved across AMPARs and TARPs. We propose a model explaining how TARPs stabilize the activated state of AMPARs and how the interactions between AMPARs and their auxiliary proteins control fast excitatory synaptic transmission.
Validation ReportPDB-ID: 5kbv

SummaryFull reportAbout validation report
DateDeposition: Jun 16, 2016 / Header (metadata) release: Jul 13, 2016 / Map release: Jul 13, 2016 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0296
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0296
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5kbv
  • Surface level: 0.0296
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8232.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.26 Å/pix.
= 252. Å
200 pix
1.26 Å/pix.
= 252. Å
200 pix
1.26 Å/pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density
Contour Level:0.0296 (by author), 0.0296 (movie #1):
Minimum - Maximum-0.046164 - 0.09551599
Average (Standard dev.)0.0013005276 (0.006060445)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 252.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0460.0960.001

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Supplemental data

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Sample components

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Entire Protein

EntireName: Protein / Number of components: 4

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Component #1: protein, Protein

ProteinName: Protein / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human) / Vector: Bacmam / Cell of expression system: HEK293

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Component #2: protein, Glutamate receptor 2

ProteinName: Glutamate receptor 2GRIA2 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 92.252344 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
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, 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.: 4 mg/ml / pH: 8
Support filmGrid coated with gold prior to use.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 299 K / Humidity: 100 % / Details: Blot force 3, 8.0 s blot time.

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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: 45 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 acquisition

Image acquisitionDetails: 30 frames across 9 seconds were collected per image.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 33152
3D reconstructionSoftware: RELION / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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