|Entry||Database: EMDB / ID: 8823|
|Title||Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin|
|Map data||Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin|
|Sample||Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin|
|Function / homology||Voltage-dependent calcium channel, gamma-2 subunit / Presynaptic depolarization and calcium channel opening / PMP-22/EMP/MP20/Claudin superfamily / Receptor, ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Voltage-dependent calcium channel, gamma subunit / Ligand-gated ion channel / PMP-22/EMP/MP20/Claudin family ...Voltage-dependent calcium channel, gamma-2 subunit / Presynaptic depolarization and calcium channel opening / PMP-22/EMP/MP20/Claudin superfamily / Receptor, ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Voltage-dependent calcium channel, gamma subunit / Ligand-gated ion channel / PMP-22/EMP/MP20/Claudin family / Receptor family ligand binding region / Ligated ion channel L-glutamate- and glycine-binding site / Periplasmic binding protein-like I / Phase 2 - plateau phase / Trafficking of AMPA receptors / Phase 0 - rapid depolarisation / LGI-ADAM interactions / 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 postsynaptic membrane neurotransmitter receptor levels / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of AMPA receptor activity / 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 / neuromuscular junction development / membrane depolarization / transmission of nerve impulse / nervous system process / 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 / positive regulation of synaptic transmission, glutamatergic / SNARE binding / positive regulation of synaptic transmission / integral component of postsynaptic membrane / regulation of membrane potential / 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 / hippocampal mossy fiber to CA3 synapse / dendrite cytoplasm / receptor internalization / synaptic vesicle membrane / integral component of presynaptic membrane / PDZ domain binding / Schaffer collateral - CA1 synapse / presynaptic membrane / terminal bouton / response to calcium ion / 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 / cytosol / Voltage-dependent calcium channel gamma-2 subunit / Glutamate receptor 2|
Function and homology information
|Source||Rattus norvegicus (Norway rat) / Mus musculus (house mouse)|
|Method||single particle reconstruction / cryo EM / 4.2 Å resolution|
|Authors||Twomey EC / Yelshanskaya MV / Grassucci RA / Frank J / Sobolevsky AI|
|Citation||Journal: 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 Report||PDB-ID: 5weo|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 10, 2017 / Header (metadata) release: Aug 2, 2017 / Map release: Aug 2, 2017 / Last update: Jul 18, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_8823.map.gz (map file in CCP4 format, 108001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.08 Å|
CCP4 map header:
-Entire Activated GluA2 complex bound to glutamate, cyclothiazide, and ST...
|Entire||Name: Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin|
Number of components: 4
-Component #1: protein, Activated GluA2 complex bound to glutamate, cyclothiazid...
|Protein||Name: Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin|
Recombinant expression: No
|Source||Species: Rattus norvegicus (Norway rat)|
|Source (engineered)||Expression System: Homo sapiens (human) / Cell of expression system: HEK293 gnti-|
-Component #2: protein, Glutamate receptor 2,Voltage-dependent calcium channel g...
|Protein||Name: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera|
Number of Copies: 4 / Recombinant expression: No
|Mass||Theoretical: 115.501969 kDa|
|Source||Species: Mus musculus (house mouse)|
|Source (engineered)||Expression System: Homo sapiens (human)|
-Component #3: ligand, GLUTAMIC ACID
|Ligand||Name: GLUTAMIC ACID / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 0.147129 kDa|
-Component #4: ligand, CYCLOTHIAZIDE
|Ligand||Name: CYCLOTHIAZIDE / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 0.389878 kDa|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 4 mg/ml / pH: 8|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 55 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 69207|
|3D reconstruction||Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF|
Details: TMD map uploaded under additional files is at 4.0 angstrom resolution.
-Atomic model buiding
|Modeling #1||Refinement space: REAL|
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