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Open data
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Basic information
Entry | Database: PDB / ID: 6njm | ||||||||||||
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Title | Architecture and subunit arrangement of native AMPA receptors | ||||||||||||
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![]() | MEMBRANE PROTEIN/Immune System / AMPA receptor / ligand gated ion channel / neurotransmitter / synapse / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Immune System complex | ||||||||||||
Function / homology | ![]() Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / membrane hyperpolarization ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / membrane hyperpolarization / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / voltage-gated calcium channel complex / spine synapse / neurotransmitter receptor localization to postsynaptic specialization membrane / protein heterotetramerization / dendritic spine neck / neuromuscular junction development / dendritic spine head / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / transmission of nerve impulse / immunoglobulin binding / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / membrane depolarization / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / synaptic cleft / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / response to fungicide / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / cytoskeletal protein binding / ionotropic glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / presynaptic active zone membrane / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / dendrite cytoplasm / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / calcium channel regulator activity / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / SNARE binding / hippocampal mossy fiber to CA3 synapse / dendritic shaft / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / cerebral cortex development / Schaffer collateral - CA1 synapse / receptor internalization / long-term synaptic potentiation / response to calcium ion / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / protein homotetramerization / chemical synaptic transmission / perikaryon / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||||||||
![]() | Gouaux, E. / Zhao, Y. | ||||||||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 898.5 KB | Display | ![]() |
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PDB format | ![]() | 693.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 118.2 KB | Display | |
Data in CIF | ![]() | 189.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9388MC ![]() 0426C ![]() 0427C ![]() 0428C ![]() 0429C ![]() 0430C ![]() 0431C ![]() 0432C ![]() 9387C ![]() 9389C ![]() 6njlC ![]() 6njnC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Glutamate receptor ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 100556.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 98783.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Antibody , 5 types, 10 molecules EGIMJNKOLP
#3: Antibody | Mass: 13039.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Antibody | Mass: 18570.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Antibody | Mass: 21038.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Antibody | Mass: 25111.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #8: Antibody | Mass: 27975.439 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein / Non-polymers , 2 types, 6 molecules FH

#11: Chemical | ChemComp-ZK1 / {[ #4: Protein | Mass: 35938.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 3 types, 10 molecules 
#9: 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 #10: Polysaccharide | Source method: isolated from a genetically manipulated source #12: Sugar | ChemComp-NAG / |
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-Details
Has protein modification | Y |
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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 |
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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 |
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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: ![]() |
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) |
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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: 99000 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |