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- EMDB-3841: Negative-stain surface of low-pH sortilin dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-3841
TitleNegative-stain surface of low-pH sortilin dimer
Map dataNegative-stain surface of low-pH sortilin dimer
Sample
  • Complex: Low-pH-induced dimer of human sSortilin extracellular domain
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / myotube differentiation / Golgi to lysosome transport / plasma membrane to endosome transport / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / nerve growth factor receptor activity / retromer complex binding / Golgi to endosome transport ...neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / myotube differentiation / Golgi to lysosome transport / plasma membrane to endosome transport / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / nerve growth factor receptor activity / retromer complex binding / Golgi to endosome transport / vesicle organization / endosome transport via multivesicular body sorting pathway / nerve growth factor binding / protein targeting to lysosome / trans-Golgi network transport vesicle / clathrin-coated vesicle / Golgi cisterna membrane / Golgi Associated Vesicle Biogenesis / endosome to lysosome transport / negative regulation of fat cell differentiation / D-glucose import / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / neuropeptide signaling pathway / clathrin-coated pit / ossification / response to insulin / endocytosis / regulation of gene expression / nuclear membrane / cytoplasmic vesicle / early endosome / lysosome / endosome membrane / G protein-coupled receptor signaling pathway / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / enzyme binding / Golgi apparatus / cell surface / membrane / plasma membrane / cytosol
Similarity search - Function
VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / : / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 13.0 Å
AuthorsJanuliene D / Thirup S / Moeller A
CitationJournal: Structure / Year: 2017
Title: Acidic Environment Induces Dimerization and Ligand Binding Site Collapse in the Vps10p Domain of Sortilin.
Authors: Dovile Januliene / Jacob Lauwring Andersen / Jeppe Achton Nielsen / Esben Meldgaard Quistgaard / Maria Hansen / Dorthe Strandbygaard / Arne Moeller / Claus Munck Petersen / Peder Madsen / Søren Skou Thirup /
Abstract: Sortilin is a neuronal receptor involved in transmembrane signaling, endocytosis, and intracellular sorting of proteins. It cycles through a number of cellular compartments where it encounters ...Sortilin is a neuronal receptor involved in transmembrane signaling, endocytosis, and intracellular sorting of proteins. It cycles through a number of cellular compartments where it encounters various acidic conditions. The crystal structure of the sortilin ectodomain has previously been determined at neutral pH. Here, we present the 3.5-Å resolution crystal structure of sortilin at pH 5.5, which represents an environment similar to that of late endosomes, where ligands are released. The structure reveals an overall distortion of the 10-bladed β-propeller domain. This distortion and specific conformational changes, caused by protonation of a number of histidine residues, render the currently known binding sites unavailable for ligand binding. Access to the binding sites is furthermore blocked by a reversible and pH-dependent formation of tight sortilin dimers, also confirmed by electron microscopy, size-exclusion chromatography, and mutational studies. This study reveals how sortilin binding sites are disrupted and explains pH-dependent ligand affinity.
History
DepositionAug 7, 2017-
Header (metadata) releaseNov 29, 2017-
Map releaseNov 29, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3841.png

Downloads & links

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Map

FileDownload / File: emd_3841.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative-stain surface of low-pH sortilin dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.15 Å/pix.
x 48 pix.
= 151.2 Å		3.15 Å/pix.
x 48 pix.
= 151.2 Å		3.15 Å/pix.
x 48 pix.
= 151.2 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.078441896 - 0.118524425
Average (Standard dev.)0.00012178843 (±0.014289872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions484848
Spacing484848
CellA=B=C: 151.20001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.153.153.15
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z151.200151.200151.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS484848
D min/max/mean-0.0780.1190.000

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Supplemental data

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Sample components

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Entire : Low-pH-induced dimer of human sSortilin extracellular domain

EntireName: Low-pH-induced dimer of human sSortilin extracellular domain
Components
  • Complex: Low-pH-induced dimer of human sSortilin extracellular domain

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Supramolecule #1: Low-pH-induced dimer of human sSortilin extracellular domain

SupramoleculeName: Low-pH-induced dimer of human sSortilin extracellular domain
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK
Molecular weightExperimental: 200 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: 5.5
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

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 55967
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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