+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2684 | |||||||||
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Title | Density map of GluA2em in complex with LY451646 and glutamate | |||||||||
Map data | Reconstruction of GluA2em activated state | |||||||||
Sample |
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Keywords | GluA2em activated state | |||||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.8 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2684.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-2684-v30.xml emd-2684.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | EMD-2684-GluA2-LY-Glu.jpg | 29 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2684 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2684 | HTTPS FTP |
-Validation report
Summary document | emd_2684_validation.pdf.gz | 204.5 KB | Display | EMDB validaton report |
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Full document | emd_2684_full_validation.pdf.gz | 203.6 KB | Display | |
Data in XML | emd_2684_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2684 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2684 | HTTPS FTP |
-Related structure data
Related structure data | 4uq6MC 2680C 2685C 2686C 2687C 2688C 2689C 4uqjC 4uqkC 4uqqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2684.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of GluA2em activated state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : GluA2em with LY451646 and glutamate
Entire | Name: GluA2em with LY451646 and glutamate |
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Components |
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-Supramolecule #1000: GluA2em with LY451646 and glutamate
Supramolecule | Name: GluA2em with LY451646 and glutamate / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 370 KDa / Theoretical: 370 KDa |
-Macromolecule #1: GluA2
Macromolecule | Name: GluA2 / type: protein_or_peptide / ID: 1 / Name.synonym: GluR2 / Oligomeric state: Tetramer / Recombinant expression: Yes |
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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: glutamate
Macromolecule | Name: glutamate / type: ligand / ID: 2 / Recombinant expression: No |
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Source (natural) | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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, 0.12 mM CHS, 0.5 mM LY451646, 100 mM NaGlutamate |
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 Timed resolved state: Protein incubated with LY451646 for 30 minutes prior to addition of glutamate, with 15 seconds elapsing before vitrification Method: Blot for 2 seconds before plunging |
-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: 1566 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |
-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: 12.8 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 16050 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera |
Details | Two copies of a 3KG2 ATD dimer assembly were fit to the EM map |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4uq6: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: C |
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Software | Name: Chimera |
Details | Two copies of a 1FTJ LBD dimer assembly were fit to the EM map |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4uq6: |