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- EMDB-3356: Activation of NMDA receptors and the mechanism of inhibition by i... -

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Basic information

Entry
Database: EMDB / ID: 3356
TitleActivation of NMDA receptors and the mechanism of inhibition by ifenprodil - Class Y
Map dataClass Y, unsharpened, unmasked map
SampleNMDA Receptor
  • (N-methyl-D-aspartate receptor ...NMDA receptor) x 2
KeywordsNMDA 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 / Receptor, ligand binding region / Synaptic adhesion-like molecules / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / RAF/MAP kinase cascade / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Ras activation upon Ca2+ influx through NMDA receptor / sensitization / regulation of postsynaptic cytosolic calcium ion concentration / cellular response to curcumin / cellular response to magnesium starvation / cellular response to corticosterone stimulus / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / 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 manganese ion / cellular response to dsRNA / apical dendrite / glycine binding / voltage-gated cation channel activity / dendrite membrane / positive regulation of glutamate secretion / multicellular organismal response to stress / NMDA glutamate receptor activity / response to carbohydrate / 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 / excitatory synapse / associative learning / regulation of MAPK cascade / behavioral fear response / long-term memory / response to amphetamine / response to cocaine / positive regulation of dendritic spine maintenance / positive regulation of excitatory postsynaptic potential / phosphatase binding / positive regulation of synaptic transmission / cerebral cortex development / response to fungicide / response to organonitrogen compound / ionotropic glutamate receptor activity / extracellularly glutamate-gated ion channel activity / cellular response to growth factor stimulus / 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 / postsynaptic membrane / protein-containing complex binding / drug binding / postsynaptic density / neuron projection / dendritic spine / response to ethanol
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 6.25 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 ReportPDB-ID: 5fxk

SummaryFull reportAbout validation report
DateDeposition: Mar 2, 2016 / Header (metadata) release: Apr 6, 2016 / Map release: May 11, 2016 / Last update: Jun 15, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5fxk
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3356.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/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
Contour Level:0.038 (by author), 0.038 (movie #1):
Minimum - Maximum-0.0173353 - 0.08615234
Average (Standard dev.)-0.00064702 (0.0065396)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0170.086-0.001

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Supplemental data

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Sample components

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Entire NMDA Receptor

EntireName: NMDA Receptor
Details: The sample was purified in the presence of agonists Glycine and L-glutamate.
Number of components: 2
Oligomeric State: One heterotetramer of 2 GluN1 and 2 GluN2B subunits
MassTheoretical: 370 kDa

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Component #1: protein, N-methyl-D-aspartate receptor GluN1

ProteinName: N-methyl-D-aspartate receptor GluN1 / a.k.a: GluN1, NR1 / Oligomeric Details: dimer / Number of Copies: 2 / Recombinant expression: Yes
MassTheoretical: 93 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Vector: Modified pFL and pUCDM / Cell of expression system: Sf9 / Strain: Sf9 CRL-1711
Source (natural)Location in cell: Plasma membane
External referencesUniProt: Glutamate receptor ionotropic, NMDA 1

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Component #2: protein, N-methyl-D-aspartate receptor GluN2B

ProteinName: N-methyl-D-aspartate receptor GluN2B / a.k.a: GluN2B, NR2B / Oligomeric Details: Dimer / Recombinant expression: Yes / Number of Copies: 2
MassTheoretical: 92 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Vector: Modified pFL and pUCDM / Cell of expression system: Sf9 / Strain: Sf9 CRL-1711
Source (natural)Location in cell: Plasma membane
External referencesUniProt: Glutamate receptor ionotropic, NMDA 2B

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml
Buffer solution: 200 mM NaCl, 20 mM HEPES pH 7.0, 10 mM Glycine, 10 mM L-Glutamate, 0.002% MNG-3
pH: 7
Support filmC-flat 1.2/1.3 Cu 400
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 90 % / Method: 3s Blot time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Aug 10, 2015
Details: 21s exposure into 70 frames, with an exposure rate of ~8 electrons/pixel/s on the camera.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal), 38168 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1200

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 15000
3D reconstructionAlgorithm: FREALIGN / Software: Unblur, CTFFIND4, FREALIGN / CTF correction: Each Particle
Details: The highest resolution included in the refinement was 8A.
Resolution: 6.25 Å / Resolution method: FSC 0.143, semi-independent

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Atomic model buiding

Modeling #1Software: Coot / Refinement protocol: flexible / Target criteria: Real Space / Refinement space: REAL
Details: The individual domains were initially fitted using coot and real space refinement was performed using Phenix
Input PDB model: 4PE5
Chain ID: A, B, C, D
Output model

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