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- EMDB-3840: Negative-stain surface of human SorCS2 dimer -

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Basic information

Entry
Database: EMDB / ID: 3840
TitleNegative-stain surface of human SorCS2 dimer
Map dataNegative-stain surface of human SorCS2 dimer
SamplehSorCS2:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / 27 Å resolution
AuthorsMoeller A / Januliene D
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Hidden Twins: SorCS Neuroreceptors Form Stable Dimers.
Authors: Dovile Januliene / Arulmani Manavalan / Peter Lund Ovesen / Karen-Marie Pedersen / Søren Thirup / Anders Nykjær / Arne Moeller
Abstract: SorCS1, SorCS2 and SorCS3 belong to the Vps10p-domain family of multiligand receptors. Genetic and functional studies have linked SorCS receptors to psychiatric disorders, Alzheimer's disease and ...SorCS1, SorCS2 and SorCS3 belong to the Vps10p-domain family of multiligand receptors. Genetic and functional studies have linked SorCS receptors to psychiatric disorders, Alzheimer's disease and type 2 diabetes, demonstrating critical roles in neuronal functionality and metabolic control. Surprisingly, their structural composition has so far not been studied. Here we have characterized SorCS1, SorCS2 and SorCS3 using biochemical methods and electron microscopy. We found that their purified extracellular domains co-exist in stable dimeric and monomeric populations. This was supported by co-immunoprecipitation experiments, where membrane-bound dimers were successfully pulled down from cell lysate. While dimers were virtually unbreakable, dimerization of the monomeric population was promoted through enzymatic deglycosylation. We conclude that post-translational modifications, specifically the degree and pattern of glycosylation, regulate the oligomeric state of the protein. Hence, cells may dictate ligand specificity by controlling the ratio between monomers and dimers and, therefore, regulate the multiple functions of SorCS receptors.
DateDeposition: Aug 7, 2017 / Header (metadata) release: Sep 6, 2017 / Map release: Sep 6, 2017 / Last update: Oct 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3840.map.gz (map file in CCP4 format, 3539 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
3.15 Å/pix.
= 302.4 Å
96 pix
3.15 Å/pix.
= 302.4 Å
96 pix
3.15 Å/pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.15 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.04070818 - 0.10535957
Average (Standard dev.)9.551392E-5 (0.007494955)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin000
Limit959595
Spacing969696
CellA=B=C: 302.40002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.153.153.15
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z302.400302.400302.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.0410.1050.000

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Supplemental data

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Sample components

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Entire hSorCS2

EntireName: hSorCS2 / Number of components: 1
MassTheoretical: 250 kDa

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Component #1: protein, hSorCS2

ProteinName: hSorCS2 / Recombinant expression: No
MassTheoretical: 250 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Mus musculus (house mouse)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.01 mg/ml / pH: 8
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 1738
3D reconstructionSoftware: RELION / Resolution: 27 Å / Resolution method: FSC 0.143 CUT-OFF

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