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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 / homology
Function and homology information


cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / EPHB-mediated forward signaling / pons maturation / regulation of cAMP/PKA signal transduction / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / regulation of cell communication ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / EPHB-mediated forward signaling / pons maturation / regulation of cAMP/PKA signal transduction / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / regulation of cell communication / auditory behavior / positive regulation of Schwann cell migration / sensitization / olfactory learning / conditioned taste aversion / response to other organism / dendritic branch / fear response / regulation of respiratory gaseous exchange / response to methylmercury / apical dendrite / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / response to manganese ion / response to carbohydrate / transmitter-gated monoatomic ion channel activity / suckling behavior / positive regulation of inhibitory postsynaptic potential / interleukin-1 receptor binding / cellular response to dsRNA / propylene metabolic process / response to glycine / cellular response to lipid / response to growth hormone / negative regulation of dendritic spine maintenance / RAF/MAP kinase cascade / heterocyclic compound binding / response to amine / positive regulation of glutamate secretion / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / response to glycoside / NMDA selective glutamate receptor complex / voltage-gated monoatomic cation channel activity / glutamate binding / neurotransmitter receptor complex / ligand-gated sodium channel activity / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / response to morphine / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / small molecule binding / receptor clustering / startle response / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / behavioral response to pain / monoatomic cation transmembrane transport / regulation of MAPK cascade / monoatomic ion channel complex / cellular response to glycine / response to magnesium ion / positive regulation of calcium ion transport into cytosol / regulation of postsynaptic membrane potential / response to electrical stimulus / action potential / extracellularly glutamate-gated ion channel activity / associative learning / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / monoatomic cation transport / social behavior / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / response to mechanical stimulus / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / long-term memory / neuron development / multicellular organismal response to stress / phosphatase binding / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / behavioral fear response / response to fungicide / monoatomic cation channel activity / synaptic cleft / calcium ion homeostasis / glutamate-gated receptor activity / cellular response to manganese ion / regulation of long-term synaptic depression / D2 dopamine receptor binding / response to cytokine / glutamate-gated calcium ion channel activity
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 / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : ...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 / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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: 5 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 1.3Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high

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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
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 / Calibrated magnification: 38168 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

SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15000 / Refinement type: HALF-MAPS REFINED AGAINST SAME DATA / Symmetry type: POINT
RefinementHighest resolution: 5 Å
Refinement stepCycle: LAST / Highest resolution: 6.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15185 0 0 0 15185

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