+Open data
-Basic information
Entry | Database: PDB / ID: 5fxg | ||||||
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Title | GLUN1B-GLUN2B NMDA RECEPTOR IN ACTIVE CONFORMATION | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / SIGNALING 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 / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / regulation of protein kinase A signaling / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / response to other organism / 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 / voltage-gated monoatomic cation channel activity / positive regulation of cysteine-type endopeptidase 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 / response to morphine / NMDA glutamate receptor activity / 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-gated calcium ion channel activity / glutamate binding / neuromuscular process / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / regulation of axonogenesis / male mating behavior / heterocyclic compound binding / suckling behavior / startle response / behavioral response to pain / response to amine / monoatomic cation transmembrane transport / receptor clustering / monoatomic cation transport / regulation of neuronal synaptic plasticity / associative learning / positive regulation of excitatory postsynaptic potential / regulation of MAPK cascade / social behavior / response to magnesium ion / ligand-gated monoatomic ion channel activity / cellular response to organic cyclic compound / extracellularly glutamate-gated ion channel activity / cellular response to glycine / excitatory synapse / positive regulation of dendritic spine maintenance / small molecule binding / neuron development / Unblocking of NMDA receptors, glutamate binding and activation / behavioral fear response / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / phosphatase binding / cellular response to manganese ion / calcium ion homeostasis / glutamate receptor binding / D2 dopamine receptor binding / prepulse inhibition / multicellular organismal response to stress / monoatomic cation channel activity / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / regulation of neuron apoptotic process / response to electrical stimulus / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å | ||||||
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 / 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 | 5fxg.cif.gz | 370.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fxg.ent.gz | 233 KB | Display | PDB format |
PDBx/mmJSON format | 5fxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fxg_validation.pdf.gz | 794.6 KB | Display | wwPDB validaton report |
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Full document | 5fxg_full_validation.pdf.gz | 830.6 KB | Display | |
Data in XML | 5fxg_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 5fxg_validation.cif.gz | 96.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxg ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxg | HTTPS FTP |
-Related structure data
Related structure data | 3352MC 3353C 3354C 3355C 3356C 5b3jC 5fxhC 5fxiC 5fxjC 5fxkC C: citing same article (ref.) M: map data used to model this data |
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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: 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 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P35439 #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.) RATTUS NORVEGICUS (Norway rat) / Plasmid: MODIFIED PFL AND PUCDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / 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
EM software |
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Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Resolution: 6.8 Å / Num. 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 | Protocol: OTHER / Space: REAL / Target criteria: REAL SPACE / Details: METHOD--REAL SPACE | ||||||||||||||||||||
Refinement | Highest resolution: 6.8 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.8 Å
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