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- PDB-5fxg: GLUN1B-GLUN2B NMDA RECEPTOR IN ACTIVE CONFORMATION -

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Basic information

Entry
Database: PDB / ID: 5fxg
TitleGLUN1B-GLUN2B NMDA RECEPTOR IN ACTIVE 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 / homologyCalmodulin-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 sourceRATTUS NORVEGICUS (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.8 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 typeGroupCategoryItemProviderType
1.0May 11, 2016Structure modelrepositoryInitial release
1.1Jun 15, 2016Structure modelDatabase references
1.2Apr 19, 2017Structure modelOther
1.3Aug 23, 2017Structure modelData collectionem_image_scans / em_software_em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3352
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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-A SPARTATE 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

EM software
IDNameVersionCategory
1CTFFIND4CTF correction
2Cootmodel fitting
3Unblurother
4FREALIGN3D reconstruction
SymmetryPoint symmetry: C2
3D reconstructionResolution: 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 buildingDetails: METHOD--REAL SPACE / Ref protocol: OTHER / Ref space: REAL / Target criteria: REAL SPACE
Least-squares processHighest resolution: 6.8 Å
Refine hist #LASTHighest resolution: 6.8 Å
Number of atoms included #LASTProtein: 12648 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 12648

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