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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: 8820
TitleGluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
Map dataGluA2 bound to antagonist ZK and GSG1L in digitonin, state 2
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 / homologyIonotropic glutamate receptor, metazoa / Periplasmic binding protein-like I / Receptor, ligand binding region / GSG1-like / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / GSG1-like protein / Receptor family ligand binding region / Ligand-gated ion channel / Ionotropic glutamate receptor ...Ionotropic glutamate receptor, metazoa / Periplasmic binding protein-like I / Receptor, ligand binding region / GSG1-like / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / GSG1-like protein / Receptor family ligand binding region / Ligand-gated ion channel / Ionotropic glutamate receptor / regulation of AMPA receptor activity / regulation of postsynaptic neurotransmitter receptor internalization / 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 / positive regulation of synaptic transmission / integral component of postsynaptic membrane / regulation of synaptic transmission, glutamatergic / response to fungicide / integral component of postsynaptic density membrane / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / ionotropic glutamate receptor activity / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / dendritic shaft / dendrite cytoplasm / receptor internalization / synaptic vesicle membrane / PDZ domain binding / integral component of presynaptic membrane / presynaptic membrane / Schaffer collateral - CA1 synapse / 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 / Germ cell-specific gene 1-like protein / Glutamate receptor 2
Function and homology information
SourceRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 4.4 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: 5wel

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: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • 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

Fileemd_8820.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
0.98 Å/pix.
= 294. Å
300 pix
0.98 Å/pix.
= 294. Å
300 pix
0.98 Å/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 Level:0.026 (by author), 0.026 (movie #1):
Minimum - Maximum-0.06896673 - 0.13429308
Average (Standard dev.)0.000805433 (0.0049637896)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.0.0.
Limit299.299.299.
Spacing300300300
CellA=B=C: 294.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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