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Open data
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Basic information
Entry | Database: PDB / ID: 5fxk | ||||||
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Title | GluN1b-GluN2B NMDA receptor structure-Class Y | ||||||
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![]() | TRANSPORT PROTEIN / SIGNALING PROTEIN / NMDA RECEPTOR / GLUTAMATE RECEPTOR / GLUN1 / GLUN2B / ION CHANNEL | ||||||
Function / homology | ![]() cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / sensitization ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / sensitization / auditory behavior / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / response to other organism / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / transmitter-gated monoatomic ion channel activity / fear response / apical dendrite / positive regulation of inhibitory postsynaptic potential / response to methylmercury / response to carbohydrate / response to glycine / propylene metabolic process / response to manganese ion / interleukin-1 receptor binding / cellular response to dsRNA / cellular response to lipid / response to glycoside / positive regulation of glutamate secretion / negative regulation of dendritic spine maintenance / response to growth hormone / regulation of monoatomic cation transmembrane transport / heterocyclic compound binding / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / glutamate binding / response to morphine / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / regulation of dendrite morphogenesis / regulation of synapse assembly / protein heterotetramerization / male mating behavior / glycine binding / response to amine / parallel fiber to Purkinje cell synapse / receptor clustering / small molecule binding / suckling behavior / regulation of long-term synaptic depression / positive regulation of reactive oxygen species biosynthetic process / startle response / monoatomic cation transmembrane transport / behavioral response to pain / positive regulation of calcium ion transport into cytosol / response to magnesium ion / associative learning / regulation of postsynaptic membrane potential / regulation of MAPK cascade / action potential / cellular response to glycine / extracellularly glutamate-gated ion channel activity / monoatomic cation transport / excitatory synapse / social behavior / positive regulation of dendritic spine maintenance / positive regulation of excitatory postsynaptic potential / response to electrical stimulus / monoatomic ion channel complex / regulation of neuronal synaptic plasticity / cellular response to manganese ion / long-term memory / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / response to mechanical stimulus / behavioral fear response / detection of mechanical stimulus involved in sensory perception of pain / synaptic cleft / multicellular organismal response to stress / neuron development / prepulse inhibition / phosphatase binding / postsynaptic density, intracellular component / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / D2 dopamine receptor binding / regulation of neuron apoptotic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å | ||||||
![]() | Tajima, N. / Karakas, E. / Grant, T. / Simorowski, N. / Diaz-Avalos, R. / Grigorieff, N. / Furukawa, H. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.1 KB | Display | ![]() |
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PDB format | ![]() | 279.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 768 KB | Display | ![]() |
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Full document | ![]() | 801.8 KB | Display | |
Data in XML | ![]() | 69.5 KB | Display | |
Data in CIF | ![]() | 112.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3356MC ![]() 3352C ![]() 3353C ![]() 3354C ![]() 3355C ![]() 5b3jC ![]() 5fxgC ![]() 5fxhC ![]() 5fxiC ![]() 5fxjC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 95220.727 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 23-868 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 92931.078 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-852 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 |
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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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 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) |
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Processing
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Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Resolution: 6.4 Å / Num. of particles: 15000 Details: SIDE CHAINS WERE NOT INCLUDED IN THE MODEL SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3356. (DEPOSITION ID: 14328). Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: REAL SPACE / Details: METHOD--REAL SPACE | ||||||||||||||||||||
Refinement | Highest resolution: 6.4 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.4 Å
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