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- EMDB-3354: Activation of NMDA receptors and the mechanism of inhibition by i... -

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Basic information

Entry
Database: EMDB / ID: EMD-3354
TitleActivation of NMDA receptors and the mechanism of inhibition by ifenprodil - Non-Active 2 confirmation
Map dataNon-Active 2 conformation, unsharpened, unfiltered map
Sample
  • Sample: NMDA Receptor
  • Protein or peptide: N-methyl-D-aspartate receptor GluN1
  • Protein or peptide: N-methyl-D-aspartate receptor GluN2B
KeywordsNMDA 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 / positive regulation of Schwann cell migration / pons maturation / sensitization / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / positive regulation of Schwann cell migration / pons maturation / sensitization / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / olfactory learning / conditioned taste aversion / dendritic branch / response to other organism / regulation of respiratory gaseous exchange / apical dendrite / fear response / regulation of ARF protein signal transduction / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / response to methylmercury / suckling behavior / response to manganese ion / response to glycine / interleukin-1 receptor binding / response to carbohydrate / propylene metabolic process / cellular response to dsRNA / cellular response to lipid / response to growth hormone / heterocyclic compound binding / negative regulation of dendritic spine maintenance / positive regulation of glutamate secretion / RAF/MAP kinase cascade / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / voltage-gated monoatomic cation channel activity / response to glycoside / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / response to morphine / regulation of axonogenesis / neuromuscular process / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / response to amine / regulation of cAMP/PKA signal transduction / receptor clustering / small molecule binding / startle response / parallel fiber to Purkinje cell synapse / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / behavioral response to pain / regulation of MAPK cascade / positive regulation of calcium ion transport into cytosol / cellular response to glycine / extracellularly glutamate-gated ion channel activity / regulation of postsynaptic membrane potential / response to magnesium ion / action potential / associative learning / response to electrical stimulus / excitatory synapse / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / social behavior / monoatomic cation transport / regulation of neuronal synaptic plasticity / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / detection of mechanical stimulus involved in sensory perception of pain / long-term memory / response to mechanical stimulus / neuron development / synaptic cleft / phosphatase binding / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / calcium ion homeostasis / glutamate-gated receptor activity / regulation of long-term synaptic depression / cell adhesion molecule binding / regulation of neuron apoptotic process
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 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, 2016-
Header (metadata) releaseApr 6, 2016-
Map releaseMay 11, 2016-
UpdateJun 15, 2016-
Current statusJun 15, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fxi
  • Surface level: 0.042
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3354.png

Downloads & links

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Map

FileDownload / File: emd_3354.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-Active 2 conformation, unsharpened, unfiltered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.042 / Movie #1: 0.042
Minimum - Maximum-0.01732981 - 0.08923765
Average (Standard dev.)-0.00063216 (±0.00659206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0170.089-0.001

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Supplemental data

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Sample components

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Entire : NMDA Receptor

EntireName: NMDA Receptor
Components
  • Sample: NMDA Receptor
  • Protein or peptide: N-methyl-D-aspartate receptor GluN1
  • Protein or peptide: N-methyl-D-aspartate receptor GluN2B

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Supramolecule #1000: NMDA Receptor

SupramoleculeName: NMDA Receptor / type: sample / ID: 1000
Details: The sample was purified in the presence of agonists Glycine and L-glutamate.
Oligomeric state: One heterotetramer of 2 GluN1 and 2 GluN2B subunits
Number unique components: 2
Molecular weightTheoretical: 370 KDa

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Macromolecule #1: N-methyl-D-aspartate receptor GluN1

MacromoleculeName: N-methyl-D-aspartate receptor GluN1 / type: protein_or_peptide / ID: 1 / Name.synonym: GluN1, NR1 / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Location in cell: Plasma membane
Molecular weightTheoretical: 93 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 CRL-1711 / Recombinant cell: Sf9 / Recombinant plasmid: Modified pFL and pUCDM
SequenceUniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: N-methyl-D-aspartate receptor GluN2B

MacromoleculeName: N-methyl-D-aspartate receptor GluN2B / type: protein_or_peptide / ID: 2 / Name.synonym: GluN2B, NR2B / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Location in cell: Plasma membane
Molecular weightTheoretical: 92 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 CRL-1711 / Recombinant cell: Sf9 / Recombinant plasmid: Modified pFL and pUCDM
SequenceUniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7
Details: 200 mM NaCl, 20 mM HEPES pH 7.0, 10 mM Glycine, 10 mM L-Glutamate, 0.002% MNG-3
GridDetails: C-flat 1.2/1.3 Cu 400
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK II / Method: 3s Blot time

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Electron beam tilt params: 0
Details21s exposure into 70 frames, with an exposure rate of ~8 electrons/pixel/s on the camera.
DateAug 10, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1200 / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each Particle
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: OTHER / Software - Name: Unblur, CTFFIND4, FREALIGN
Details: The highest resolution included in the refinement was 8A.
Number images used: 16000

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Atomic model buiding 1

Initial modelPDB ID:

4pe5


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: Coot
DetailsThe individual domains were initially fitted using coot and real space refinement was performed using Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Real Space
Output model

PDB-5fxi:
GluN1b-GluN2B NMDA receptor structure in non-active-2 conformation

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