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- EMDB-8823: Activated GluA2 complex bound to glutamate, cyclothiazide, and ST... -

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Basic information

Entry
Database: EMDB / ID: 8823
TitleActivated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
Map dataActivated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
SampleActivated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
  • Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
  • (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) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsTwomey EC / Yelshanskaya MV / Grassucci RA / Frank J / Sobolevsky AI
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
Validation ReportPDB-ID: 5weo

SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2017 / Header (metadata) release: Aug 2, 2017 / Map release: Aug 2, 2017 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5weo
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8823.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.08 Å/pix.
= 324. Å
300 pix
1.08 Å/pix.
= 324. Å
300 pix
1.08 Å/pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.09160006 - 0.16419825
Average (Standard dev.)0.0006511989 (0.0055219787)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.0.0.
Limit299.299.299.
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0920.1640.001

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Supplemental data

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Sample components

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Entire Activated GluA2 complex bound to glutamate, cyclothiazide, and ST...

EntireName: Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
Number of components: 4

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Component #1: protein, Activated GluA2 complex bound to glutamate, cyclothiazid...

ProteinName: Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293 gnti-

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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 chimera
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 115.501969 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, GLUTAMIC ACID

LigandName: GLUTAMIC ACID / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.147129 kDa

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Component #4: ligand, CYCLOTHIAZIDE

LigandName: CYCLOTHIAZIDE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.389878 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
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: 55 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: 69207
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
Details: TMD map uploaded under additional files is at 4.0 angstrom resolution.

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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