|Entry||Database: PDB / ID: 5fxg|
|Title||GLUN1B-GLUN2B NMDA RECEPTOR IN ACTIVE CONFORMATION|
|Keywords||TRANSPORT PROTEIN / SIGNALING PROTEIN / NMDA RECEPTOR / GLUTAMATE RECEPTOR / GLUN1 / GLUN2B / ION CHANNEL|
|Function / homology||Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor / Ionotropic glutamate receptor, metazoa / Receptor, ligand binding region / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Periplasmic binding protein-like I / Receptor family ligand binding region / Ligand-gated ion channel ...Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor / Ionotropic glutamate receptor, metazoa / Receptor, ligand binding region / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Periplasmic binding protein-like I / Receptor family ligand binding region / Ligand-gated ion channel / N-methyl D-aspartate receptor 2B3 C-terminus / Ligated ion channel L-glutamate- and glycine-binding site / EPHB-mediated forward signaling / Unblocking of NMDA receptor, glutamate binding and activation / CREB phosphorylation through the activation of CaMKII / Ras activation upon Ca2+ influx through NMDA receptor / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / sensitization / cellular response to curcumin / regulation of postsynaptic cytosolic calcium ion concentration / cellular response to magnesium starvation / cellular response to corticosterone stimulus / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / D2 dopamine receptor binding / NMDA selective glutamate receptor signaling pathway / dendritic branch / response to other organism / calcium ion transmembrane import into cytosol / cellular response to lipid / glutamate-gated calcium ion channel activity / neurotransmitter binding / action potential / cellular response to dsRNA / apical dendrite / cellular response to manganese ion / glutamate receptor binding / glycine binding / voltage-gated cation channel activity / positive regulation of glutamate secretion / multicellular organismal response to stress / response to carbohydrate / NMDA glutamate receptor activity / glutamate binding / dendrite membrane / NMDA selective glutamate receptor complex / interleukin-1 receptor binding / positive regulation of reactive oxygen species biosynthetic process / synaptic membrane / positive regulation of cysteine-type endopeptidase activity / response to methylmercury / response to amine / response to manganese ion / cellular response to forskolin / response to magnesium ion / positive regulation of calcium ion transport into cytosol / response to growth hormone / receptor clustering / extracellularly glutamate-gated ion channel activity / regulation of MAPK cascade / ionotropic glutamate receptor binding / excitatory synapse / behavioral fear response / associative learning / synaptic cleft / long-term memory / response to amphetamine / positive regulation of dendritic spine maintenance / response to cocaine / positive regulation of excitatory postsynaptic potential / phosphatase binding / positive regulation of synaptic transmission / cerebral cortex development / response to fungicide / ionotropic glutamate receptor activity / cellular response to growth factor stimulus / hippocampus development / response to organonitrogen compound / cellular response to organic cyclic compound / ionotropic glutamate receptor signaling pathway / response to electrical stimulus / cellular response to amino acid stimulus / cell adhesion molecule binding / positive regulation of cell death / memory / response to toxic substance / regulation of long-term neuronal synaptic plasticity / response to mechanical stimulus / response to cytokine / terminal bouton / presynaptic membrane / Z disc / rhythmic process / protein heterotetramerization / response to organic cyclic compound / response to calcium ion / learning or memory / protein tetramerization / beta-catenin binding / scaffold protein binding|
Function and homology information
|Specimen source||RATTUS NORVEGICUS (Norway rat)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.8 Å resolution|
|Authors||Tajima, N. / Karakas, E. / Grant, T. / Simorowski, N. / Diaz-Avalos, R. / Grigorieff, N. / Furukawa, 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
SummaryFull reportAbout validation report
|Date||Deposition: Mar 2, 2016 / Release: May 11, 2016|
|Structure viewer||Molecule: |
Downloads & links
A: N-METHYL-D-ASPARTATE RECEPTOR GLUN1
B: N-METHYL-D-ASPARTATE RECEPTOR GLUN2B
C: N-METHYL-D-ASPARTATE RECEPTOR GLUN1
D: N-METHYL-D-ASPARTATE RECEPTOR GLUN2B
Mass: 95220.727 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 23-868 / Mutation: YES / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid name: MODIFIED PFL AND PUCDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P35439
Mass: 92931.078 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-852 / Mutation: YES / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid name: MODIFIED PFL AND PUCDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q00960
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: NMDA RECEPTOR / Type: COMPLEX|
|Buffer solution||Name: 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3|
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
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope 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 / Calibrated magnification: 38168 / 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)|
|Symmetry||Point symmetry: C2|
|3D reconstruction||Resolution: 6.8 Å / Number of particles: 12000|
Details: SIDE CHAINS WERE NOT INCLUDED IN THE MODEL. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3352. (DEPOSITION ID: 14321).
Symmetry type: POINT
|Atomic model building||Details: METHOD--REAL SPACE / Ref protocol: OTHER / Ref space: REAL / Target criteria: REAL SPACE|
|Least-squares process||Highest resolution: 6.8 Å|
|Refine hist #LAST||Highest resolution: 6.8 Å|
|Number of atoms included #LAST||Protein: 12648 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 12648|
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