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- PDB-5fwy: Crystal structure of the AMPA receptor GluA2/A3 N-terminal domain... -
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Basic information
Entry | Database: PDB / ID: 5fwy | ||||||
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Title | Crystal structure of the AMPA receptor GluA2/A3 N-terminal domain heterodimer | ||||||
![]() | (GLUTAMATE RECEPTOR ...) x 2 | ||||||
![]() | TRANSPORT PROTEIN | ||||||
Function / homology | ![]() Trafficking of AMPA receptors / Synaptic adhesion-like molecules / spine synapse / protein heterotetramerization / dendritic spine neck / dendritic spine head / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity ...Trafficking of AMPA receptors / Synaptic adhesion-like molecules / spine synapse / protein heterotetramerization / dendritic spine neck / 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 / 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 / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / synaptic cleft / 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 / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / 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 / 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 / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
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![]() | Herguedas, B. / Garcia-Nafria, J. / Greger, I.H. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 594 KB | Display | ![]() |
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PDB format | ![]() | 491.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 496.8 KB | Display | ![]() |
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Full document | ![]() | 507.8 KB | Display | |
Data in XML | ![]() | 55.2 KB | Display | |
Data in CIF | ![]() | 77.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8090C ![]() 8091C ![]() 5fwxC ![]() 5ideC ![]() 5idfC ![]() 3hsyS ![]() 3o21S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-GLUTAMATE RECEPTOR ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 43731.359 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-400 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 45093.953 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-403 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 1 types, 10 molecules 
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 361 molecules 




#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.18 % / Description: NONE |
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Crystal grow | Details: 14-16 % PEG 3350, 0.27 M AMMONIUM SULPHATE AND 0.1 M BICINE PH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Dec 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→41.75 Å / Num. obs: 100269 / % possible obs: 90.4 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.12→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 87.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3HSY AND 3O21 Resolution: 2.12→41.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.006 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.088 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→41.76 Å
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