[English] 日本語
Yorodumi- EMDB-2687: Density map of GluA2em desensitized state in complex with quisqua... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2687 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Density map of GluA2em desensitized state in complex with quisqualate (class 2) | |||||||||
Map data | Reconstruction of GluA2em desensitized state (class 2) | |||||||||
Sample |
| |||||||||
Keywords | Membrane 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 | |||||||||
Biological species | Rattus norvegicus (Norway rat) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 25.9 Å | |||||||||
Authors | Meyerson JR / Kumar J / Chittori S / Rao P / Pierson J / Bartesaghi A / Mayer ML / Subramaniam S | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2687.map.gz | 4.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2687-v30.xml emd-2687.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | EMD-2687-GluA2-Quis-class2.jpg | 20.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2687 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2687 | HTTPS FTP |
-Related structure data
Related structure data | 2680C 2684C 2685C 2686C 2688C 2689C 4uq6C 4uqjC 4uqkC 4uqqC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2687.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of GluA2em desensitized state (class 2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.406 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : GluA2em with quisqualate ligand
Entire | Name: GluA2em with quisqualate ligand |
---|---|
Components |
|
-Supramolecule #1000: GluA2em with quisqualate ligand
Supramolecule | Name: GluA2em with quisqualate ligand / type: sample / ID: 1000 / Number unique components: 2 |
---|---|
Molecular weight | Experimental: 370 KDa / Theoretical: 370 KDa |
-Macromolecule #1: GluA2
Macromolecule | Name: GluA2 / type: protein_or_peptide / ID: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Rattus norvegicus (Norway rat) / synonym: Rat |
Molecular weight | Experimental: 370 KDa / Theoretical: 370 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: pFastBac1 |
Sequence | UniProtKB: Glutamate receptor 2 |
-Macromolecule #2: quisqualate
Macromolecule | Name: quisqualate / type: ligand / ID: 2 / Recombinant expression: No |
---|---|
Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.8 mg/mL |
---|---|
Buffer | pH: 8 Details: 150 mM NaCl, 20 mM Tris pH 8.0, 0.75 mM DDM, 0.12 mM CHS, 1 mM quisqualic acid |
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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Date | Aug 1, 2013 |
Image recording | Category: 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 |
-Image processing
CTF correction | Details: Each particle |
---|---|
Final reconstruction | Applied 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 |
Details | The particles were selected interactively at the computer terminal. |