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Yorodumi- PDB-4uqk: Electron density map of GluA2em in complex with quisqualate and L... -
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-Basic information
Entry | Database: PDB / ID: 4uqk | ||||||
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Title | Electron density map of GluA2em in complex with quisqualate and LY451646 | ||||||
Components | GLUTAMATE RECEPTOR 2GRIA2 | ||||||
Keywords | TRANSPORT PROTEIN / GLUA2EM RESTORED ACTIVE STATE | ||||||
Function / homology | Function and homology information spine synapse / dendritic spine head / dendritic spine neck / Activation of AMPA receptors / response to lithium ion / cellular response to glycine / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine head / dendritic spine neck / Activation of AMPA receptors / response to lithium ion / cellular response to glycine / perisynaptic space / 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 / positive regulation of synaptic transmission / presynaptic active zone membrane / response to fungicide / glutamate-gated receptor activity / 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 / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / 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 / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / chemical synaptic transmission / perikaryon / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / 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: 16.4 Å | ||||||
Authors | Meyerson, J.R. / Kumar, J. / Chittori, S. / Rao, P. / Pierson, J. / Bartesaghi, A. / Mayer, M.L. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4uqk.cif.gz | 416.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uqk.ent.gz | 332.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqk ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqk | HTTPS FTP |
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-Related structure data
Related structure data | 2689MC 2680C 2684C 2685C 2686C 2687C 2688C 4uq6C 4uqjC 4uqqC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 93105.156 Da / Num. of mol.: 4 / Fragment: RESIDUES 22-847 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P19491 #2: Chemical | ChemComp-QUS / ( Sequence details | SEQUENCE IS FROM PDB 3KG2 TRUNCATED TO THAT USED TO FIT EM MAPS | |
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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: GLU A2 ATD AND GLUA2 LBD / Type: COMPLEX |
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Buffer solution | pH: 8 |
Specimen | Conc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Aug 1, 2013 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 1303 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 16.4 Å / Num. of particles: 4795 Details: FOUR ASSEMBLIES CONSISTING OF TWO ATD DIMERS FROM PDB 3KG2 AND TWO LBD DIMERS FROM PDB 1MM7 WERE FIT AS INDEPENDENT RIGID BODIES TO EM MAPS GEOMETRY AND STEREOCHEMISTRY OUTLIERS ARE THOSE ...Details: FOUR ASSEMBLIES CONSISTING OF TWO ATD DIMERS FROM PDB 3KG2 AND TWO LBD DIMERS FROM PDB 1MM7 WERE FIT AS INDEPENDENT RIGID BODIES TO EM MAPS GEOMETRY AND STEREOCHEMISTRY OUTLIERS ARE THOSE PRESENT IN THE PDB ENTRIES USED FOR RIGID BODY FITTING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2689. (DEPOSITION ID: 12609). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY | ||||||||||||
Atomic model building | PDB-ID: 1MM7 | ||||||||||||
Refinement | Highest resolution: 16.4 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 16.4 Å
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