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- PDB-5weo: Activated GluA2 complex bound to glutamate, cyclothiazide, and ST... -

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Basic information

Entry
Database: PDB / ID: 5weo
TitleActivated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
ComponentsGlutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
KeywordsTRANSPORT PROTEIN / Ion channel
Function / homologyReceptor family ligand binding region / Voltage-dependent calcium channel, gamma-2 subunit / Periplasmic binding protein-like I / Ligated ion channel L-glutamate- and glycine-binding site / Presynaptic depolarization and calcium channel opening / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Voltage-dependent calcium channel, gamma subunit / Ligand-gated ion channel / Trafficking of AMPA receptors / Phase 0 - rapid depolarisation ...Receptor family ligand binding region / Voltage-dependent calcium channel, gamma-2 subunit / Periplasmic binding protein-like I / Ligated ion channel L-glutamate- and glycine-binding site / Presynaptic depolarization and calcium channel opening / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Voltage-dependent calcium channel, gamma subunit / Ligand-gated ion channel / Trafficking of AMPA receptors / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / LGI-ADAM interactions / PMP-22/EMP/MP20/Claudin superfamily / Receptor, ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / PMP-22/EMP/MP20/Claudin family / regulation of postsynaptic neurotransmitter receptor activity / neurotransmitter receptor transport, postsynaptic endosome to lysosome / channel regulator activity / neurotransmitter receptor internalization / postsynaptic density membrane / nervous system process / regulation of AMPA receptor activity / postsynaptic neurotransmitter receptor diffusion trapping / somatodendritic compartment / neuromuscular junction development / voltage-gated calcium channel complex / membrane hyperpolarization / transmission of nerve impulse / membrane depolarization / voltage-gated calcium channel activity / AMPA glutamate receptor activity / asymmetric synapse / regulation of membrane potential / 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 / SNARE binding / regulation of synaptic transmission, glutamatergic / response to fungicide / synaptic vesicle membrane / ionotropic glutamate receptor activity / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / dendritic shaft / PDZ domain binding / dendrite cytoplasm / receptor internalization / terminal bouton / presynaptic membrane / chemical synaptic transmission / establishment of protein localization / growth cone / protein tetramerization / signaling receptor activity / amyloid-beta binding / postsynaptic membrane / ATPase binding / perikaryon / postsynaptic density / dendritic spine / neuron projection / synapse / cell junction / neuronal cell body / dendrite / intracellular / endoplasmic reticulum membrane / protein kinase binding / integral component of plasma membrane / cell surface / protein-containing complex / identical protein binding / Voltage-dependent calcium channel gamma-2 subunit / Glutamate receptor 2
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsTwomey, E.C. / Yelshanskaya, M.V. / Grassucci, R.A. / Frank, J. / Sobolevsky, A.I.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Sep 13, 2017Structure modelAuthor supporting evidence / Database referencescitation / pdbx_audit_support_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
1.2Jul 18, 2018Structure modelData collection / Experimental preparationem_sample_support_em_sample_support.grid_type

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Assembly

Deposited unit
A: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
B: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
C: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
D: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,15612
Polyers462,0084
Non-polymers2,1488
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)30380
ΔGint (kcal/M)-237
Surface area (Å2)191300

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Components

#1: Protein/peptide
Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit chimera / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / Neuronal voltage-gated calcium channel gamma-2 subunit / Stargazin / Transmembrane AMPAR regulatory protein gamma-2 / TARP gamma-2


Mass: 115501.969 Da / Num. of mol.: 4
Fragment: UNP P19491 residues 25-847, UNP O88602 2-208 linked via LINKER GT
Mutation: N241E, V382L, G384E, N385D, V758L
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse)
Gene: Gria2, Glur2, Cacng2, Stg / Cell line (production host): HEK293 gnti- / Production host: Homo sapiens (human) / References: UniProt: P19491, UniProt: O88602
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Mass: 147.129 Da / Num. of mol.: 4 / Formula: C5H9NO4 / Glutamic acid
#3: Chemical
ChemComp-CYZ / CYCLOTHIAZIDE / 3-BICYCLO[2.2.1]HEPT-5-EN-2-YL-6-CHLORO-3,4- DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE-7-SULFONAMIDE 1,1 DIOXIDE


Mass: 389.878 Da / Num. of mol.: 4 / Formula: C14H16ClN3O4S2 / Cyclothiazide

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Cell: HEK293 gnti- / Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 4 mg/ml
Details: Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 8 sec. / Electron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 69207
Details: TMD map uploaded under additional files is at 4.0 angstrom resolution.
Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00831856
ELECTRON MICROSCOPYf_angle_d0.97743066
ELECTRON MICROSCOPYf_dihedral_angle_d10.88718730
ELECTRON MICROSCOPYf_chiral_restr0.0554774
ELECTRON MICROSCOPYf_plane_restr0.0075408

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