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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 / homologyIonotropic glutamate receptor, L-glutamate and glycine-binding domain / Ionotropic glutamate receptor, metazoa / Ligand-gated ion channel / Voltage-dependent calcium channel, gamma-2 subunit / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily / Receptor family ligand binding region / Receptor, ligand binding region / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor ...Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ionotropic glutamate receptor, metazoa / Ligand-gated ion channel / Voltage-dependent calcium channel, gamma-2 subunit / PMP-22/EMP/MP20/Claudin family / PMP-22/EMP/MP20/Claudin superfamily / Receptor family ligand binding region / Receptor, ligand binding region / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Periplasmic binding protein-like I / Presynaptic depolarization and calcium channel opening / Trafficking of AMPA receptors / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / LGI-ADAM interactions / Voltage-dependent calcium channel, gamma subunit / positive regulation of protein localization to basolateral plasma membrane / eye blink reflex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / cerebellar mossy fiber / channel regulator activity / neurotransmitter receptor internalization / regulation of AMPA receptor activity / positive regulation of AMPA receptor activity / regulation of postsynaptic neurotransmitter receptor activity / postsynaptic neurotransmitter receptor diffusion trapping / membrane hyperpolarization / voltage-gated calcium channel complex / somatodendritic compartment / protein targeting to membrane / nervous system process / neuromuscular junction development / membrane depolarization / transmission of nerve impulse / postsynaptic density membrane / voltage-gated calcium channel activity / AMPA glutamate receptor activity / asymmetric synapse / ionotropic glutamate receptor binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / response to lithium ion / regulation of receptor recycling / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / SNARE binding / integral component of postsynaptic membrane / positive regulation of synaptic transmission / integral component of postsynaptic density membrane / regulation of synaptic transmission, glutamatergic / response to fungicide / ionotropic glutamate receptor activity / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / synaptic vesicle membrane / dendritic shaft / dendrite cytoplasm / integral component of presynaptic membrane / receptor internalization / PDZ domain binding / Schaffer collateral - CA1 synapse / terminal bouton / presynaptic membrane / response to calcium ion / establishment of protein localization / protein tetramerization / growth cone / chemical synaptic transmission / amyloid-beta binding / ATPase binding / signaling receptor activity / perikaryon / 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 / cytosol / Voltage-dependent calcium channel gamma-2 subunit / Glutamate receptor 2
Function and homology information
SourceRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 7.8 Å resolution
AuthorsTwomey EC / Yelshanskaya MV / Grassucci RA / 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: 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
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 367.19998 Å
α=β=γ: 90.0 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
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 115.515984 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, 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: 8 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (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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