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- EMDB-0347: Apo form metabotropic glutamate receptor 5 with Nanobody 43 -

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Basic information

Entry
Database: EMDB / ID: 0347
TitleApo form metabotropic glutamate receptor 5 with Nanobody 43
Map dataApo form metabotropic glutamate receptor 5 with Nanobody 43, primary map
SampleMetabotropic Glutamate Receptor 5 - Nb43 Complex:
Metabotropic Glutamate Receptor 5 / Nanobody 43Single-domain antibody
SourceHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / 7.9 Å resolution
AuthorsKoehl A / Hu H / Feng D / Zhang Y / Sun B / Kobilka TS / Pardon E / Steyaert J / Mathiesen JM / Skiniotis G / 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
DateDeposition: Nov 20, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Feb 6, 2019 / Last update: Feb 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.054
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.054
  • 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_0347.map.gz (map file in CCP4 format, 6913 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
2.58 Å/pix.
= 309.6 Å
120 pix
2.58 Å/pix.
= 309.6 Å
120 pix
2.58 Å/pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.58 Å
Density
Contour Level:0.054 (by author), 0.054 (movie #1):
Minimum - Maximum-0.018538713 - 0.11647756
Average (Standard dev.)0.0010566172 (0.0109877335)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin0.00.00.0
Limit119.0119.0119.0
Spacing120120120
CellA=B=C: 309.59998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.582.582.58
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z309.600309.600309.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-16-63-38
NX/NY/NZ727975
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.0190.1160.001

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Supplemental data

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Sample components

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Entire Metabotropic Glutamate Receptor 5 - Nb43 Complex

EntireName: Metabotropic Glutamate Receptor 5 - Nb43 Complex
Details: Complex between metabotropic glutamate receptor 5 and Nb43
Number of components: 3

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Component #1: protein, Metabotropic Glutamate Receptor 5 - Nb43 Complex

ProteinName: Metabotropic Glutamate Receptor 5 - Nb43 Complex
Details: Complex between metabotropic glutamate receptor 5 and Nb43
Recombinant expression: No
MassTheoretical: 220 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
Details: Polypeptide encoding metabotropic glutamate receptor 5
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, Nanobody 43

ProteinName: Nanobody 43Single-domain antibody / Details: Nanobody 43Single-domain antibody / Recombinant expression: No
SourceSpecies: Lama glama (llama)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 10 mg/ml / pH: 7.5
VitrificationCryogen name: ETHANE

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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: 29000.0 X (nominal), 58139.0 X (calibrated) / 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: 44831
3D reconstructionSoftware: RELION / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF

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