+Open data
-Basic information
Entry | Database: PDB / ID: 5fxj | ||||||
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Title | GluN1b-GluN2B NMDA receptor structure-Class X | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / NMDA RECEPTOR / GLUTAMATE RECEPTOR / GLUN1 / GLUN2B / ION CHANNEL | ||||||
Function / homology | Function and homology information neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / NMDA selective glutamate receptor signaling pathway / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / pons maturation / regulation of cell communication ...neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / NMDA selective glutamate receptor signaling pathway / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Assembly and cell surface presentation of NMDA receptors / olfactory learning / regulation of protein kinase A signaling / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / apical dendrite / response to other organism / fear response / response to methylmercury / voltage-gated monoatomic cation channel activity / positive regulation of cysteine-type endopeptidase activity / response to morphine / glutamate-gated calcium ion channel activity / cellular response to dsRNA / response to carbohydrate / regulation of monoatomic cation transmembrane transport / negative regulation of dendritic spine maintenance / interleukin-1 receptor binding / cellular response to lipid / positive regulation of glutamate secretion / NMDA glutamate receptor activity / response to growth hormone / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / response to manganese ion / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / male mating behavior / regulation of dendrite morphogenesis / regulation of axonogenesis / heterocyclic compound binding / receptor clustering / suckling behavior / startle response / behavioral response to pain / regulation of neuronal synaptic plasticity / response to amine / monoatomic cation transmembrane transport / regulation of MAPK cascade / social behavior / small molecule binding / associative learning / response to magnesium ion / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / excitatory synapse / extracellularly glutamate-gated ion channel activity / cellular response to organic cyclic compound / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / positive regulation of dendritic spine maintenance / glutamate receptor binding / regulation of postsynaptic membrane potential / behavioral fear response / multicellular organismal response to stress / phosphatase binding / calcium ion homeostasis / D2 dopamine receptor binding / cellular response to manganese ion / prepulse inhibition / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of synaptic transmission / regulation of neuron apoptotic process / response to electrical stimulus / response to mechanical stimulus / glutamate-gated receptor activity / synaptic cleft / presynaptic active zone membrane / response to fungicide / cellular response to forskolin / monoatomic cation channel activity / sensory perception of pain Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.25 Å | ||||||
Authors | Tajima, N. / Karakas, E. / Grant, T. / Simorowski, N. / Diaz-Avalos, R. / Grigorieff, N. / Furukawa H, H. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Activation of NMDA receptors and the mechanism of inhibition by ifenprodil. Authors: Nami Tajima / Erkan Karakas / Timothy Grant / Noriko Simorowski / Ruben Diaz-Avalos / Nikolaus Grigorieff / Hiro Furukawa / Abstract: The physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed ...The physiology of N-methyl-d-aspartate (NMDA) receptors is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed mainly of GluN1 and GluN2 subunits. Activation of NMDA receptors requires binding of neurotransmitter agonists to a ligand-binding domain (LBD) and structural rearrangement of an amino-terminal domain (ATD). Recent crystal structures of GluN1-GluN2B NMDA receptors bound to agonists and an allosteric inhibitor, ifenprodil, represent the allosterically inhibited state. However, how the ATD and LBD move to activate the NMDA receptor ion channel remains unclear. Here we applied X-ray crystallography, single-particle electron cryomicroscopy and electrophysiology to rat NMDA receptors to show that, in the absence of ifenprodil, the bi-lobed structure of GluN2 ATD adopts an open conformation accompanied by rearrangement of the GluN1-GluN2 ATD heterodimeric interface, altering subunit orientation in the ATD and LBD and forming an active receptor conformation that gates the ion channel. | ||||||
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 | 5fxj.cif.gz | 429.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fxj.ent.gz | 277.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxj ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxj | HTTPS FTP |
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-Related structure data
Related structure data | 3355MC 3352C 3353C 3354C 3356C 5b3jC 5fxgC 5fxhC 5fxiC 5fxkC 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
#1: Protein | Mass: 95220.727 Da / Num. of mol.: 2 / Fragment: ATD.LBD, TMD, UNP RESIDUES 23-868 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: MODIFIED PFL AND PUCDM / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Variant (production host): CRL-1711 / References: UniProt: P35439 #2: Protein | Mass: 92931.078 Da / Num. of mol.: 2 / Fragment: ATD, LBD, TMD, UNP RESIDUES 27-852 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: MODIFIED PFL AND PUCDM / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Variant (production host): CRL-1711 / References: UniProt: Q00960 |
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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: NMDA RECEPTOR / Type: COMPLEX |
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Buffer solution | Name: 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3 pH: 7 Details: 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK II / 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 10, 2015 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 38168 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 100 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||
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3D reconstruction | Resolution: 6.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14000 / Refinement type: HALF-MAPS REFINED AGAINST SAME DATA / Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 6.25 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.5 Å
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