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- EMDB-2685: Density map of GluK2 desensitized state in complex with 2S,4R-4-m... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2685 | |||||||||
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Title | Density map of GluK2 desensitized state in complex with 2S,4R-4-methylglutamate | |||||||||
![]() | Reconstruction of GluK2 desensitized state | |||||||||
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![]() | Membrane Protein / Ion Channel / Glutamate Receptor | |||||||||
Function / homology | ![]() mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / positive regulation of synaptic transmission / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / synapse / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | |||||||||
![]() | Meyerson JR / Kumar J / Chittori S / Rao P / Pierson J / Bartesaghi A / Mayer ML / Subramaniam S | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.7 KB 9.7 KB | Display Display | ![]() |
Images | ![]() | 48.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uqqMC ![]() 2680C ![]() 2684C ![]() 2686C ![]() 2687C ![]() 2688C ![]() 2689C ![]() 4uq6C ![]() 4uqjC ![]() 4uqkC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of GluK2 desensitized state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.406 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : GluAK2 with 2S,4R-4-methylglutamate
Entire | Name: GluAK2 with 2S,4R-4-methylglutamate |
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Components |
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-Supramolecule #1000: GluAK2 with 2S,4R-4-methylglutamate
Supramolecule | Name: GluAK2 with 2S,4R-4-methylglutamate / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 400 KDa / Theoretical: 400 KDa |
-Macromolecule #1: GluK2
Macromolecule | Name: GluK2 / type: protein_or_peptide / ID: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 400 KDa / Theoretical: 400 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Glutamate receptor ionotropic, kainate 2 |
-Macromolecule #2: 2S,4R-4-methylglutamate
Macromolecule | Name: 2S,4R-4-methylglutamate / type: ligand / ID: 2 / Recombinant expression: No |
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Source (natural) | Organism: synthetic construct (others) |
Chemical component information | ![]() ChemComp-SYM: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.8 mg/mL |
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Buffer | pH: 8 Details: 150 mM NaCl, 20 mM Tris pH 8.0, 0.75 mM DDM, 1 mM 2S,4R-4-methylglutamate |
Grid | 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 ...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). |
Vitrification | Cryogen 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
Microscope | FEI TITAN KRIOS |
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Date | Aug 1, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 4837 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | Particles were selected interactively at the computer terminal |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 21360 |