[English] 日本語
Yorodumi- PDB-8p3t: Homomeric GluA1 in tandem with TARP gamma-3, desensitized conform... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p3t | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Homomeric GluA1 in tandem with TARP gamma-3, desensitized conformation 1 | ||||||||||||
Components |
| ||||||||||||
Keywords | MEMBRANE PROTEIN / AMPAR / ion channels / neurotransmission | ||||||||||||
Function / homology | Function and homology information Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / 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 ...Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / 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 / neuron spine / regulation of AMPA receptor activity / neurotransmitter receptor internalization / channel regulator activity / response to arsenic-containing substance / cellular response to dsRNA / postsynaptic neurotransmitter receptor diffusion trapping / dendritic spine membrane / Synaptic adhesion-like molecules / glutamate-gated calcium ion channel activity / neurotransmitter receptor localization to postsynaptic specialization membrane / long-term synaptic depression / cellular response to peptide hormone stimulus / protein kinase A binding / spinal cord development / neuronal cell body membrane / Activation of AMPA receptors / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / cellular response to organic cyclic compound / adenylate cyclase binding / ionotropic glutamate receptor complex / excitatory synapse / asymmetric synapse / regulation of receptor recycling / G-protein alpha-subunit binding / voltage-gated calcium channel activity / Unblocking of NMDA receptors, glutamate binding and activation / neuronal action potential / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / glutamate receptor binding / protein targeting / positive regulation of synaptic transmission / long-term memory / response to electrical stimulus / glutamate-gated receptor activity / presynaptic active zone membrane / beta-2 adrenergic receptor binding / response to fungicide / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / synapse assembly / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of synaptic transmission, glutamatergic / 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 / long-term synaptic potentiation / cellular response to amino acid stimulus / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / regulation of synaptic plasticity / neuromuscular junction / protein localization / response to organic cyclic compound / receptor internalization / recycling endosome / response to toxic substance / cerebral cortex development / cellular response to growth factor stimulus / response to peptide hormone / synaptic vesicle membrane / small GTPase binding / recycling endosome membrane / G-protein beta-subunit binding / cell-cell junction / synaptic vesicle / presynapse / response to estradiol / presynaptic membrane / amyloid-beta binding / early endosome membrane / cell body / scaffold protein binding / postsynapse / chemical synaptic transmission / postsynaptic membrane Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å | ||||||||||||
Authors | Zhang, D. / Krieger, J. / Yamashita, K. / Greger, I. | ||||||||||||
Funding support | United Kingdom, European Union, 3items
| ||||||||||||
Citation | Journal: Nature / Year: 2023 Title: Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor. Authors: Danyang Zhang / Josip Ivica / James M Krieger / Hinze Ho / Keitaro Yamashita / Imogen Stockwell / Rozbeh Baradaran / Ondrej Cais / Ingo H Greger / Abstract: AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. ...AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. Despite their prominent expression throughout interneurons and glia, their role in long-term potentiation and their involvement in a range of neuropathologies, structural information for GluA2-lacking receptors is currently absent. Here we determine and characterize cryo-electron microscopy structures of the GluA1 homotetramer, fully occupied with TARPγ3 auxiliary subunits (GluA1/γ3). The gating core of both resting and open-state GluA1/γ3 closely resembles GluA2-containing receptors. However, the sequence-diverse N-terminal domains (NTDs) give rise to a highly mobile assembly, enabling domain swapping and subunit re-alignments in the ligand-binding domain tier that are pronounced in desensitized states. These transitions underlie the unique kinetic properties of GluA1. A GluA2 mutant (F231A) increasing NTD dynamics phenocopies this behaviour, and exhibits reduced synaptic responses, reflecting the anchoring function of the AMPAR NTD at the synapse. Together, this work underscores how the subunit-diverse NTDs determine subunit arrangement, gating properties and ultimately synaptic signalling efficiency among AMPAR subtypes. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8p3t.cif.gz | 468.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8p3t.ent.gz | 354 KB | Display | PDB format |
PDBx/mmJSON format | 8p3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p3t_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8p3t_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8p3t_validation.xml.gz | 71.3 KB | Display | |
Data in CIF | 8p3t_validation.cif.gz | 108.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/8p3t ftp://data.pdbj.org/pub/pdb/validation_reports/p3/8p3t | HTTPS FTP |
-Related structure data
Related structure data | 17394MC 8c1pC 8c1qC 8c1rC 8c1sC 8c2hC 8c2iC 8p3qC 8p3sC 8p3uC 8p3vC 8p3wC 8p3xC 8p3yC 8p3zC 8pivC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 102661.930 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria1, Glur1 / Production host: Homo sapiens (human) / References: UniProt: P19490 #2: Protein | Mass: 35435.332 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacng3 / Production host: Homo sapiens (human) / References: UniProt: Q8VHX0 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Homomeric GluA1 AMPA receptor in tandem with TARP gamma 3, plus 1mM quisqualate Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72104 / Symmetry type: POINT |