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Yorodumi- PDB-5idf: Cryo-EM structure of GluA2/3 AMPA receptor heterotetramer (model II) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5idf | ||||||
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Title | Cryo-EM structure of GluA2/3 AMPA receptor heterotetramer (model II) | ||||||
Components |
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Keywords | SIGNALING PROTEIN / AMPA glutamate receptor | ||||||
Function / homology | Function and homology information chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / 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 / regulation of postsynaptic membrane potential / synaptic cleft / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / 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 / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / monoatomic ion transmembrane transport / 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 / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / 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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.31 Å | ||||||
Authors | Herguedas, B. / Garcia-Nafria, J. / Fernandez-Leiro, R. / Greger, I.H. | ||||||
Citation | Journal: Science / Year: 2016 Title: Structure and organization of heteromeric AMPA-type glutamate receptors. Authors: Beatriz Herguedas / Javier García-Nafría / Ondrej Cais / Rafael Fernández-Leiro / James Krieger / Hinze Ho / Ingo H Greger / Abstract: AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we ...AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we report the first AMPAR heteromer structures, which deviate substantially from existing GluA2 homomer structures. Crystal structures of the GluA2/3 and GluA2/4 N-terminal domains reveal a novel compact conformation with an alternating arrangement of the four subunits around a central axis. This organization is confirmed by cysteine cross-linking in full-length receptors, and it permitted us to determine the structure of an intact GluA2/3 receptor by cryogenic electron microscopy. Two models in the ligand-free state, at resolutions of 8.25 and 10.3 angstroms, exhibit substantial vertical compression and close associations between domain layers, reminiscent of N-methyl-D-aspartate receptors. Model 1 resembles a resting state and model 2 a desensitized state, thus providing snapshots of gating transitions in the nominal absence of ligand. Our data reveal organizational features of heteromeric AMPARs and provide a framework to decipher AMPAR architecture and signaling. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5idf.cif.gz | 410 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5idf.ent.gz | 262.3 KB | Display | PDB format |
PDBx/mmJSON format | 5idf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/5idf ftp://data.pdbj.org/pub/pdb/validation_reports/id/5idf | HTTPS FTP |
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-Related structure data
Related structure data | 8091MC 8090C 5fwxC 5fwyC 5ideC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 97663.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The sequence corresponds to mature rat GluA2 (residues 22-883, isoform Flip, edited at R/G and Q/R sites) with a Myc tag after the first residue and the N292C mutation Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pIRES2-eGFP / Cell line (production host): HEK293 gntI- / Production host: Homo sapiens (human) / References: UniProt: P19491 #2: Protein | Mass: 99075.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The sequence corresponds to the mature rat GluA3 subunit (residues 23-888, Flip isoform) with a Flag tag after the first residue and mutated at R439G and R265C Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria3, Glur3 / Plasmid: prk5 / Cell line (production host): HEK293 GntI- / Production host: Homo sapiens (human) / References: UniProt: P19492 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: AMPA GluA2/3 heterotetramer / Type: COMPLEX Details: Full-length GluA2/3 heterotetramer containing the A2_N292C and A3_265C mutations Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.4 MDa / Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 GntI- / Plasmid: prk5 and pIRES2-EGFP |
Buffer solution | pH: 7.4 / Details: 25 mM Tris pH 7.4, 0.25 % DDM, 150 mM NaCl |
Specimen | Conc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Incubated for 1 minute, blotted for 3 seconds |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 28409 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 25 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 980 |
EM imaging optics | Energyfilter name: GIF Quantum / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Movie frames/image: 20 / Used frames/image: 1-20 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 107939 | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 10.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14119 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: For GluA2 chains (A,C), 2 copies of GluA2 NTD (3HSY) and two copies of GluA2 LBD (1FTO) were fitted. For GluA3 chains (B,D), 2 copies of GluA3NTD (3O21) and two copies of GluA2 LBD (3UA8) ...Details: For GluA2 chains (A,C), 2 copies of GluA2 NTD (3HSY) and two copies of GluA2 LBD (1FTO) were fitted. For GluA3 chains (B,D), 2 copies of GluA3NTD (3O21) and two copies of GluA2 LBD (3UA8) were fitted.For the TMD region, the 4 chains of 3KG2 TMD (residues 509-544 594-629 784-817) were fitted as a rigid body. After fitting the sequence was corrected including mutations and side chains were removed. | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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