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- PDB-5fxh: GluN1b-GluN2B NMDA receptor in non-active-1 conformation -

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Basic information

Entry
Database: PDB / ID: 5fxh
TitleGluN1b-GluN2B NMDA receptor in non-active-1 conformation
Components
  • N-METHYL-D-ASPARTATE RECEPTOR GLUN1
  • N-METHYL-D-ASPARTATE RECEPTOR GLUN2B
KeywordsTRANSPORT PROTEIN / SIGNALING PROTEIN / NMDA RECEPTOR / GLUTAMATE RECEPTOR / GLUN1 / GLUN2B / ION CHANNEL
Function / homologyPeriplasmic binding protein-like I / Ionotropic glutamate receptor, metazoa / N-methyl D-aspartate receptor 2B3 C-terminus / Ligand-gated ion channel / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Receptor family ligand binding region / EPHB-mediated forward signaling / Unblocking of NMDA receptor, glutamate binding and activation / Ionotropic glutamate receptor / Ligated ion channel L-glutamate- and glycine-binding site ...Periplasmic binding protein-like I / Ionotropic glutamate receptor, metazoa / N-methyl D-aspartate receptor 2B3 C-terminus / Ligand-gated ion channel / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Receptor family ligand binding region / EPHB-mediated forward signaling / Unblocking of NMDA receptor, glutamate binding and activation / Ionotropic glutamate receptor / Ligated ion channel L-glutamate- and glycine-binding site / CREB phosphorylation through the activation of CaMKII / Ras activation upon Ca2+ influx through NMDA receptor / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Receptor, ligand binding region / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / cellular response to curcumin / regulation of postsynaptic cytosolic calcium ion concentration / sensitization / cellular response to corticosterone stimulus / cellular response to magnesium starvation / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / dendritic branch / NMDA selective glutamate receptor signaling pathway / response to other organism / calcium ion transmembrane import into cytosol / glutamate-gated calcium ion channel activity / cellular response to lipid / neurotransmitter binding / apical dendrite / action potential / cellular response to manganese ion / cellular response to dsRNA / multicellular organismal response to stress / glycine binding / voltage-gated cation channel activity / dendrite membrane / positive regulation of glutamate secretion / response to carbohydrate / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate 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 / response to magnesium ion / cellular response to forskolin / positive regulation of calcium ion transport into cytosol / synaptic cleft / response to growth hormone / receptor clustering / associative learning / excitatory synapse / regulation of MAPK cascade / behavioral fear response / long-term memory / response to amphetamine / response to cocaine / positive regulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / phosphatase binding / positive regulation of synaptic transmission / cerebral cortex development / response to fungicide / response to organonitrogen compound / ionotropic glutamate receptor activity / cellular response to growth factor stimulus / extracellularly glutamate-gated ion channel activity / hippocampus development / cellular response to organic cyclic compound / ionotropic glutamate receptor signaling pathway / response to electrical stimulus / positive regulation of cell death / cellular response to amino acid stimulus / memory / regulation of long-term neuronal synaptic plasticity / presynaptic membrane / response to cytokine / response to toxic substance / response to mechanical stimulus / terminal bouton / response to calcium ion / Z disc / rhythmic process / response to organic cyclic compound / protein heterotetramerization / learning or memory / protein tetramerization / protein-containing complex binding / postsynaptic membrane / drug binding / postsynaptic density / neuron projection / dendritic spine / response to ethanol
Function and homology information
Specimen sourceRATTUS NORVEGICUS (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5 Å resolution
AuthorsTajima, N. / Karakas, E. / Grant, T. / Simorowski, N. / Diaz-Avalos, R. / Grigorieff, N. / Furukawa, H.
CitationJournal: 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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 2, 2016 / Release: May 11, 2016
RevisionDateData content typeGroupProviderType
1.0May 11, 2016Structure modelrepositoryInitial release
1.1Jun 15, 2016Structure modelDatabase references
1.2Apr 19, 2017Structure modelOther

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Structure visualization

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)376,3044
Polyers376,3044
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide N-METHYL-D-ASPARTATE RECEPTOR GLUN1 / GLUN1 / GLUTAMATE NMDA RECEPTOR SUBUNIT ZETA-1 / N-METHYL-D-ASPARTATE RECEPTOR SUBUNIT NR1 / NMD-R1 / N-METHYL-D-ASPARTATE RECEPTOR GLUN1


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
#2: Protein/peptide N-METHYL-D-ASPARTATE RECEPTOR GLUN2B / GLUN1 / GLUTAMATE NMDA RECEPTOR SUBUNIT ZETA-1 / N-METHYL-D-ASPARTATE RECEPTOR SUBUNIT NR1 / NMD-R1 / N-METHYL-D-ASPARTATE RECEPTOR GLUN1


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NMDA RECEPTOR / Type: COMPLEX
Buffer solutionName: 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
pH: 7
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: 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
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Aug 10, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Calibrated magnification: 38168 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SymmetryPoint symmetry: C2
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 15000 / Refinement type: HALF-MAPS REFINED AGAINST SAME DATA / Symmetry type: POINT
Least-squares processHighest resolution: 6.1 Å
Refine hist #LASTHighest resolution: 6.1 Å
Number of atoms included #LASTProtein: 15185 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 15185

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