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

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Basic information

Entry
Database: EMDB / ID: EMD-3840
TitleNegative-stain surface of human SorCS2 dimer
Map dataNegative-stain surface of human SorCS2 dimer
Sample
  • Complex: hSorCS2
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsMoeller A / Januliene D
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Danish Council for Independent Research4093-00238B Denmark
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
DepositionAug 7, 2017-
Header (metadata) releaseSep 6, 2017-
Map releaseSep 6, 2017-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

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

emd_3840.png

Downloads & links

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Map

FileDownload / File: emd_3840.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative-stain surface of human SorCS2 dimer
Voxel sizeX=Y=Z: 3.15 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.04070818 - 0.10535957
Average (Standard dev.)0.00009551392 (±0.007494955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: hSorCS2

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Supramolecule #1: hSorCS2

SupramoleculeName: hSorCS2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Mus musculus (house mouse)
Molecular weightTheoretical: 250 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

Concentration0.01 mg/mL
BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

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

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Tilt angle: 50 degrees
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 1738

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