+Open data
-Basic information
Entry | Database: PDB / ID: 6njn | |||||||||
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Title | Architecture and subunit arrangement of native AMPA receptors | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / AMPA receptor / ligand gated ion channel / neurotransmitter / synapse | |||||||||
Function / homology | Function and homology information Presynaptic depolarization and calcium channel opening / chemical synaptic transmission, postsynaptic / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion ...Presynaptic depolarization and calcium channel opening / chemical synaptic transmission, postsynaptic / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / LGI-ADAM interactions / myosin V binding / Trafficking of AMPA receptors / regulation of AMPA receptor activity / neuron spine / neurotransmitter receptor internalization / channel regulator activity / membrane hyperpolarization / response to arsenic-containing substance / cellular response to dsRNA / postsynaptic neurotransmitter receptor diffusion trapping / dendritic spine membrane / Synaptic adhesion-like molecules / nervous system process / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / protein targeting to membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / long-term synaptic depression / cellular response to peptide hormone stimulus / voltage-gated calcium channel complex / protein kinase A binding / neuromuscular junction development / neuronal cell body membrane / spinal cord development / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / regulation of postsynaptic membrane neurotransmitter receptor levels / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / membrane depolarization / AMPA glutamate receptor complex / adenylate cyclase binding / kainate selective glutamate receptor activity / cellular response to organic cyclic compound / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / excitatory synapse / calcium channel regulator activity / asymmetric synapse / G-protein alpha-subunit binding / regulation of receptor recycling / neuronal action potential / voltage-gated calcium channel activity / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / long-term memory / response to electrical stimulus / synaptic cleft / presynaptic active zone membrane / glutamate-gated receptor activity / beta-2 adrenergic receptor binding / response to fungicide / monoatomic ion transmembrane transport / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / SNARE binding / response to cocaine / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / regulation of membrane potential / long-term synaptic potentiation / protein tetramerization / cellular response to amino acid stimulus / postsynaptic density membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Rattus norvegicus (Norway rat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Gouaux, E. / Zhao, Y. | |||||||||
Citation | Journal: Science / Year: 2019 Title: Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM. Authors: Yan Zhao / Shanshuang Chen / Adam C Swensen / Wei-Jun Qian / Eric Gouaux / Abstract: Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric ...Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo-electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating. | |||||||||
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 | 6njn.cif.gz | 876.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6njn.ent.gz | 689.7 KB | Display | PDB format |
PDBx/mmJSON format | 6njn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6njn_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6njn_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6njn_validation.xml.gz | 119.8 KB | Display | |
Data in CIF | 6njn_validation.cif.gz | 188.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/6njn ftp://data.pdbj.org/pub/pdb/validation_reports/nj/6njn | HTTPS FTP |
-Related structure data
Related structure data | 9389MC 0426C 0427C 0428C 0429C 0430C 0431C 0432C 9387C 9388C 6njlC 6njmC 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
-Glutamate receptor ... , 3 types, 4 molecules ABDC
#1: Protein | Mass: 101518.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P19490 | ||
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#2: Protein | Mass: 98783.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P19491 #3: Protein | | Mass: 100556.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P19492 |
-Antibody , 5 types, 9 molecules EGIJNKOLM
#4: Antibody | Mass: 13039.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) #6: Antibody | | Mass: 27511.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #7: Antibody | Mass: 25111.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) #8: Antibody | Mass: 27975.439 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) #9: Antibody | Mass: 19081.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) |
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-Protein / Non-polymers , 2 types, 6 molecules FH
#12: Chemical | ChemComp-ZK1 / {[ #5: Protein | Mass: 35938.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q71RJ2 |
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-Sugars , 3 types, 11 molecules
#10: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #11: Polysaccharide | Source method: isolated from a genetically manipulated source #13: Sugar | |
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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
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Source (natural) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 54 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161000 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |