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- EMDB-0346: Metabotropic Glutamate Receptor 5 Apo Form -

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Basic information

Entry
Database: EMDB / ID: 0346
TitleMetabotropic Glutamate Receptor 5 Apo Form
Map data
SampleMetabotropic Glutamate Receptor 5 in Nanodiscs:
Metabotropic glutamate receptor 5 / ligand
Function / homologyGPCR, family 3, conserved site / Homer-binding domain of metabotropic glutamate receptor / Periplasmic binding protein-like I / Metabotropic glutamate receptor, Homer-binding domain / GPCR, family 3, metabotropic glutamate receptor / Receptor family ligand binding region / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, metabotropic glutamate receptor 5 / GPCR, family 3 / Receptor, ligand binding region ...GPCR, family 3, conserved site / Homer-binding domain of metabotropic glutamate receptor / Periplasmic binding protein-like I / Metabotropic glutamate receptor, Homer-binding domain / GPCR, family 3, metabotropic glutamate receptor / Receptor family ligand binding region / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, metabotropic glutamate receptor 5 / GPCR, family 3 / Receptor, ligand binding region / GPCR, family 3, nine cysteines domain / G-protein coupled receptors family 3 signature 1. / GPCR, family 3, nine cysteines domain superfamily / G-protein coupled receptors family 3 signature 2. / GPCR family 3, C-terminal / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 profile. / G alpha (q) signalling events / Class C/3 (Metabotropic glutamate/pheromone receptors) / Neurexins and neuroligins / 7 transmembrane sweet-taste receptor of 3 GCPR / regulation of translational elongation / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / protein tyrosine kinase activator activity / postsynaptic modulation of chemical synaptic transmission / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / regulation of intracellular calcium activated chloride channel activity / glutamate receptor activity / postsynaptic density membrane / G protein-coupled receptor activity / modulation of age-related behavioral decline / calcium-mediated signaling using intracellular calcium source / synapse organization / protein tyrosine kinase binding / regulation of synaptic transmission, glutamatergic / locomotory behavior / cognition / regulation of protein phosphorylation / learning / regulation of long-term neuronal synaptic plasticity / positive regulation of protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / learning or memory / cellular response to amyloid-beta / regulation of translation / chemical synaptic transmission / neuron projection / G protein-coupled receptor signaling pathway / integral component of plasma membrane / plasma membrane / cytoplasm / Metabotropic glutamate receptor 5
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsKoehl A / Hu H / Feng D / Sun B / Weis WI / Skiniotis GS / Mathiesen JM / Kobilka BK
CitationJournal: Nature / Year: 2019
Title: Structural insights into the activation of metabotropic glutamate receptors.
Authors: Antoine Koehl / Hongli Hu / Dan Feng / Bingfa Sun / Yan Zhang / Michael J Robertson / Matthew Chu / Tong Sun Kobilka / Toon Laermans / Jan Steyaert / Jeffrey Tarrasch / Somnath Dutta / Rasmus Fonseca / William I Weis / Jesper M Mathiesen / Georgios Skiniotis / Brian K Kobilka
Validation ReportPDB-ID: 6n52

SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2018 / Header (metadata) release: Jan 23, 2019 / Map release: Jan 23, 2019 / Last update: Feb 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.031
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.031
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6n52
  • Surface level: 0.031
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0346.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.06 Å/pix.
= 271.36 Å
256 pix
1.06 Å/pix.
= 271.36 Å
256 pix
1.06 Å/pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.031 (by author), 0.031 (movie #1):
Minimum - Maximum-0.056266032 - 0.13191475
Average (Standard dev.)0.00044996676 (0.005848763)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
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-0.0560.1320.000

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Supplemental data

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Sample components

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Entire Metabotropic Glutamate Receptor 5 in Nanodiscs

EntireName: Metabotropic Glutamate Receptor 5 in Nanodiscs / Details: Metabotropic Glutamate Receptor 5 in Nanodiscs / Number of components: 3

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Component #1: protein, Metabotropic Glutamate Receptor 5 in Nanodiscs

ProteinName: Metabotropic Glutamate Receptor 5 in Nanodiscs / Details: Metabotropic Glutamate Receptor 5 in Nanodiscs / Recombinant expression: No
MassTheoretical: 200 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Strain: Sf9

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Component #2: protein, Metabotropic glutamate receptor 5

ProteinName: Metabotropic glutamate receptor 5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 97.677945 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 7 mg/ml
Buffer solution: 100mM NaCl, 20 mM HEPES pH 7.5, 5uM FFMTEB added as a negative allosteric modulator.
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %
Details: Addition 0.0005% Amphipol A8-35was added to sample prior to apply to grid; 3.5ul sample was applied; blot for 1s before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal), 47169.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 123096
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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