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- EMDB-3708: Negative-stain surface of SorCS1 monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-3708
TitleNegative-stain surface of SorCS1 monomer
Map dataNegative stain surface of mSorCS1 monomer
Sample
  • Complex: SorCS1
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
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.
History
DepositionMay 5, 2017-
Header (metadata) releaseJun 14, 2017-
Map releaseSep 6, 2017-
UpdateApr 1, 2020-
Current statusApr 1, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3708.png

Downloads & links

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Map

FileDownload / File: emd_3708.map.gz / Format: CCP4 / Size: 85.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain surface of mSorCS1 monomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.29 Å/pix.
x 28 pix.
= 176.12 Å		6.29 Å/pix.
x 28 pix.
= 176.12 Å		6.29 Å/pix.
x 28 pix.
= 176.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.06862277 - 0.21573825
Average (Standard dev.)0.0036887347 (±0.01998518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-14-14-14
Dimensions282828
Spacing282828
CellA=B=C: 176.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.296.296.29
M x/y/z282828
origin x/y/z0.0000.0000.000
length x/y/z176.120176.120176.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS-14-14-14
NC/NR/NS282828
D min/max/mean-0.0690.2160.004

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Supplemental data

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Sample components

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Entire : SorCS1

EntireName: SorCS1
Components
  • Complex: SorCS1

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Supramolecule #1: SorCS1

SupramoleculeName: SorCS1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
Molecular weightExperimental: 140 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3f6k

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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