+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 / regulation of postsynaptic cytosolic calcium ion concentration / sensory organ development / sensitization / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration ...neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / 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 / response to hydrogen sulfide / Assembly and cell surface presentation of NMDA receptors / olfactory learning / regulation of protein kinase A signaling / conditioned taste aversion / dendritic branch / response to other organism / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / positive regulation of inhibitory postsynaptic potential / apical dendrite / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / fear response / response to methylmercury / positive regulation of cysteine-type endopeptidase activity / voltage-gated monoatomic cation channel activity / cellular response to dsRNA / response to carbohydrate / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / interleukin-1 receptor binding / cellular response to lipid / NMDA glutamate receptor activity / response to morphine / positive regulation of glutamate secretion / response to growth hormone / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / response to manganese ion / NMDA selective glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / glutamate binding / neuromuscular process / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / regulation of synapse assembly / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of axonogenesis / regulation of dendrite morphogenesis / male mating behavior / heterocyclic compound binding / suckling behavior / receptor clustering / startle response / behavioral response to pain / response to amine / small molecule binding / regulation of neuronal synaptic plasticity / action potential / monoatomic cation transmembrane transport / monoatomic cation transport / associative learning / positive regulation of excitatory postsynaptic potential / regulation of MAPK cascade / response to magnesium ion / social behavior / ligand-gated monoatomic ion channel activity / cellular response to organic cyclic compound / excitatory synapse / extracellularly glutamate-gated ion channel activity / cellular response to glycine / positive regulation of dendritic spine maintenance / behavioral fear response / neuron development / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / postsynaptic density, intracellular component / cellular response to manganese ion / glutamate receptor binding / D2 dopamine receptor binding / multicellular organismal response to stress / long-term memory / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / monoatomic cation channel activity / detection of mechanical stimulus involved in sensory perception of pain / calcium ion homeostasis / regulation of neuron apoptotic process / synaptic cleft / response to electrical stimulus / response to mechanical stimulus / glutamate-gated receptor activity 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
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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
Summary document | 5fxj_validation.pdf.gz | 833.8 KB | Display | wwPDB validaton report |
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Full document | 5fxj_full_validation.pdf.gz | 872.3 KB | Display | |
Data in XML | 5fxj_validation.xml.gz | 69.9 KB | Display | |
Data in CIF | 5fxj_validation.cif.gz | 113.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxj ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxj | HTTPS FTP |
-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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1 |
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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 FIELD / 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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