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- PDB-5fxk: GluN1b-GluN2B NMDA receptor structure-Class Y -

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Basic information

Entry
Database: PDB / ID: 5fxk
TitleGluN1b-GluN2B NMDA receptor structure-Class Y
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 / homology
Function and homology information


cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / sensitization / cellular response to curcumin / auditory behavior / pons maturation / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / positive regulation of Schwann cell migration ...cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / sensitization / cellular response to curcumin / auditory behavior / pons maturation / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / protein localization to postsynaptic membrane / conditioned taste aversion / response to carbohydrate / fear response / suckling behavior / olfactory learning / response to other organism / response to methylmercury / response to hydrogen sulfide / dendritic branch / regulation of ARF protein signal transduction / response to glycoside / transmitter-gated monoatomic ion channel activity / response to manganese ion / apical dendrite / interleukin-1 receptor binding / cellular response to dsRNA / regulation of respiratory gaseous exchange / cellular response to lipid / propylene metabolic process / response to glycine / response to growth hormone / RAF/MAP kinase cascade / positive regulation of inhibitory postsynaptic potential / heterocyclic compound binding / neuromuscular process / neurotransmitter receptor complex / negative regulation of dendritic spine maintenance / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / NMDA selective glutamate receptor complex / glutamate binding / regulation of axonogenesis / ligand-gated sodium channel activity / startle response / behavioral fear response / voltage-gated monoatomic cation channel activity / response to morphine / positive regulation of glutamate secretion / calcium ion transmembrane import into cytosol / regulation of synapse assembly / male mating behavior / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / regulation of dendrite morphogenesis / small molecule binding / behavioral response to pain / receptor clustering / glycine binding / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / social behavior / regulation of neuronal synaptic plasticity / associative learning / neuron development / regulation of postsynaptic membrane potential / regulation of MAPK cascade / response to electrical stimulus / extracellularly glutamate-gated ion channel activity / multicellular organismal response to stress / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / action potential / detection of mechanical stimulus involved in sensory perception of pain / cellular response to glycine / response to magnesium ion / Unblocking of NMDA receptors, glutamate binding and activation / response to mechanical stimulus / glutamate receptor binding / monoatomic cation transport / prepulse inhibition / ligand-gated monoatomic ion channel activity / phosphatase binding / long-term memory / adult locomotory behavior / calcium ion homeostasis / regulation of long-term neuronal synaptic plasticity / postsynaptic density, intracellular component / response to fungicide / monoatomic cation channel activity / sensory perception of pain / cellular response to manganese ion / glutamate-gated receptor activity / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / response to amphetamine
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å
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 /
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
DepositionMar 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_image_scans / em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • EMDB-3356
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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
Polymers376,3044
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D 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
pH: 7
Details: 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3
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
MicroscopyModel: FEI TITAN KRIOS / Date: Aug 10, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / 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 (2 fold cyclic)
3D reconstructionResolution: 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 buildingProtocol: OTHER / Space: REAL / Target criteria: REAL SPACE / Details: METHOD--REAL SPACE
RefinementHighest resolution: 6.4 Å
Refinement stepCycle: LAST / Highest resolution: 6.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15386 0 0 0 15386

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