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- EMDB-8231: Cryo-EM structure of GluA2-2xSTZ complex at 7.8 Angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: 8231
TitleCryo-EM structure of GluA2-2xSTZ complex at 7.8 Angstrom resolution
Map dataCryo-EM structure of GluA2-2xSTZ complex at 7.8 Angstrom resolution
SampleProtein
  • Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
  • (ligand) x 2
Function / homologyVoltage-dependent calcium channel, gamma subunit / Presynaptic depolarization and calcium channel opening / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / PMP-22/EMP/MP20/Claudin superfamily / Voltage-dependent calcium channel, gamma-2 subunit / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Periplasmic binding protein-like I / Ligand-gated ion channel / PMP-22/EMP/MP20/Claudin family ...Voltage-dependent calcium channel, gamma subunit / Presynaptic depolarization and calcium channel opening / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / PMP-22/EMP/MP20/Claudin superfamily / Voltage-dependent calcium channel, gamma-2 subunit / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Periplasmic binding protein-like I / Ligand-gated ion channel / PMP-22/EMP/MP20/Claudin family / Receptor family ligand binding region / Receptor, ligand binding region / Ligated ion channel L-glutamate- and glycine-binding site / Phase 2 - plateau phase / Phase 0 - rapid depolarisation / Trafficking of AMPA receptors / LGI-ADAM interactions / regulation of postsynaptic neurotransmitter receptor activity / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / neurotransmitter receptor transport, postsynaptic endosome to lysosome / channel regulator activity / cerebellar mossy fiber / neurotransmitter receptor internalization / nervous system process / postsynaptic density membrane / regulation of AMPA receptor activity / positive regulation of AMPA receptor activity / postsynaptic neurotransmitter receptor diffusion trapping / voltage-gated calcium channel complex / somatodendritic compartment / neuromuscular junction development / membrane hyperpolarization / protein targeting to membrane / transmission of nerve impulse / membrane depolarization / voltage-gated calcium channel activity / AMPA glutamate receptor activity / asymmetric synapse / ionotropic glutamate receptor binding / regulation of membrane potential / 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 / synaptic vesicle membrane / ionotropic glutamate receptor activity / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / dendritic shaft / dendrite cytoplasm / receptor internalization / PDZ domain binding / terminal bouton / presynaptic membrane / response to calcium ion / chemical synaptic transmission / establishment of protein localization / protein tetramerization / growth cone / signaling receptor activity / amyloid-beta binding / postsynaptic membrane / ATPase binding / perikaryon / postsynaptic density / dendritic spine / synapse / cell junction / dendrite / neuronal cell body / endoplasmic reticulum membrane / protein kinase binding / integral component of plasma membrane / cell surface / protein-containing complex / identical protein binding / cytosol / Voltage-dependent calcium channel gamma-2 subunit / Glutamate receptor 2
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 7.8 Å resolution
AuthorsTwomey EC / Yelshanskaya MV
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: 5kbu

SummaryFull reportAbout validation report
DateDeposition: Jun 10, 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: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5kbu
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8231.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
1.02 Å/pix.
= 367.2 Å
360 pix
1.02 Å/pix.
= 367.2 Å
360 pix
1.02 Å/pix.
= 367.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density
Contour Level:0.019 (by author), 0.019 (movie #1):
Minimum - Maximum-0.021717712 - 0.054960977
Average (Standard dev.)0.00033139347 (0.0026047712)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 367.19998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z367.200367.200367.200
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/NS360360360
D min/max/mean-0.0220.0550.000

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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,Voltage-dependent calcium channel g...

ProteinName: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit
Recombinant expression: No
MassTheoretical: 115.515984 kDa
Source (engineered)Expression System: Mus musculus (house mouse)

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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.: 2 mg/ml / pH: 8
Support filmGrid coated with gold prior to use.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 % / Details: 3 blot force, 8.0 s blot time

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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: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionDetails: 40 frames were collected across 8 seconds per image.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 10293
3D reconstructionResolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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