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- EMDB-2687: Density map of GluA2em desensitized state in complex with quisqua... -

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Basic information

Entry
Database: EMDB / ID: EMD-2687
TitleDensity map of GluA2em desensitized state in complex with quisqualate (class 2)
Map dataReconstruction of GluA2em desensitized state (class 2)
Sample
  • Sample: GluA2em with quisqualate ligand
  • Protein or peptide: GluA2
  • Ligand: quisqualateQuisqualic acid
KeywordsMembrane Protein / Ion Channel / Glutamate Receptor
Function / homology
Function and homology information


spine synapse / dendritic spine head / dendritic spine neck / Activation of AMPA receptors / response to lithium ion / cellular response to glycine / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine head / dendritic spine neck / Activation of AMPA receptors / response to lithium ion / cellular response to glycine / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / presynaptic active zone membrane / response to fungicide / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / chemical synaptic transmission / perikaryon / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.9 Å
AuthorsMeyerson JR / Kumar J / Chittori S / Rao P / Pierson J / Bartesaghi A / Mayer ML / Subramaniam S
CitationJournal: Nature / Year: 2014
Title: Structural mechanism of glutamate receptor activation and desensitization.
Authors: Joel R Meyerson / Janesh Kumar / Sagar Chittori / Prashant Rao / Jason Pierson / Alberto Bartesaghi / Mark L Mayer / Sriram Subramaniam /
Abstract: Ionotropic glutamate receptors are ligand-gated ion channels that mediate excitatory synaptic transmission in the vertebrate brain. To gain a better understanding of how structural changes gate ion ...Ionotropic glutamate receptors are ligand-gated ion channels that mediate excitatory synaptic transmission in the vertebrate brain. To gain a better understanding of how structural changes gate ion flux across the membrane, we trapped rat AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) and kainate receptor subtypes in their major functional states and analysed the resulting structures using cryo-electron microscopy. We show that transition to the active state involves a 'corkscrew' motion of the receptor assembly, driven by closure of the ligand-binding domain. Desensitization is accompanied by disruption of the amino-terminal domain tetramer in AMPA, but not kainate, receptors with a two-fold to four-fold symmetry transition in the ligand-binding domains in both subtypes. The 7.6 Å structure of a desensitized kainate receptor shows how these changes accommodate channel closing. These findings integrate previous physiological, biochemical and structural analyses of glutamate receptors and provide a molecular explanation for key steps in receptor gating.
History
DepositionJun 21, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseAug 13, 2014-
UpdateOct 29, 2014-
Current statusOct 29, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0518
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0518
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2687.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of GluA2em desensitized state (class 2)
Voxel sizeX=Y=Z: 1.406 Å
Density
Contour LevelBy AUTHOR: 0.0518 / Movie #1: 0.0518
Minimum - Maximum-0.01741747 - 0.14792216
Average (Standard dev.)0.00566268 (±0.02004018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin100100100
Dimensions200200200
Spacing200200200
CellA=B=C: 281.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4061.4061.406
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z281.200281.200281.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS100100100
NC/NR/NS200200200
D min/max/mean-0.0170.1480.006

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Supplemental data

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Sample components

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Entire : GluA2em with quisqualate ligand

EntireName: GluA2em with quisqualate ligand
Components
  • Sample: GluA2em with quisqualate ligand
  • Protein or peptide: GluA2
  • Ligand: quisqualateQuisqualic acid

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Supramolecule #1000: GluA2em with quisqualate ligand

SupramoleculeName: GluA2em with quisqualate ligand / type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 370 KDa / Theoretical: 370 KDa

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Macromolecule #1: GluA2

MacromoleculeName: GluA2 / type: protein_or_peptide / ID: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat
Molecular weightExperimental: 370 KDa / Theoretical: 370 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: pFastBac1
SequenceUniProtKB: Glutamate receptor 2

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Macromolecule #2: quisqualate

MacromoleculeName: quisqualate / type: ligand / ID: 2 / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 8
Details: 150 mM NaCl, 20 mM Tris pH 8.0, 0.75 mM DDM, 0.12 mM CHS, 1 mM quisqualic acid
GridDetails: Vitrified specimens were prepared by adding 2.5 uL of liganded protein at 1.8 mg/ml to R2/2 holey carbon grids (Quantifoil, Jena, Germany) rendered hydrophilic by chemical treatment to ...Details: Vitrified specimens were prepared by adding 2.5 uL of liganded protein at 1.8 mg/ml to R2/2 holey carbon grids (Quantifoil, Jena, Germany) rendered hydrophilic by chemical treatment to enable particle distribution into the holes (Meyerson JR, Rao P, Kumar K, Chittori S, Banerjee S, Pierson J, Mayer ML, and Subramaniam S, manuscript in preparation).
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateAug 1, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 888 / Average electron dose: 25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.9 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 5997
DetailsThe particles were selected interactively at the computer terminal.

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