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

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Basic information

Entry
Database: EMDB / ID: 3841
TitleNegative-stain surface of low-pH sortilin dimer
Map dataNegative-stain surface of low-pH sortilin dimer
SampleLow-pH-induced dimer of human sSortilin extracellular domain:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / 13 Å resolution
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.
DateDeposition: Aug 7, 2017 / Header (metadata) release: Nov 29, 2017 / Map release: Nov 29, 2017 / Last update: Jan 31, 2018

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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

Downloads & links

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Map

Fileemd_3841.map.gz (map file in CCP4 format, 257 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
48 pix
3.15 Å/pix.
= 151.2 Å
48 pix
3.15 Å/pix.
= 151.2 Å
48 pix
3.15 Å/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
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.13784511 - 0.12959523
Average (Standard dev.)0.0019867404 (0.02570774)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions404040
Origin000
Limit393939
Spacing404040
CellA=B=C: 126 Å
α=β=γ: 90 deg.

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/NZ
NX/NY/NZ
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
Number of components: 1
MassExperimental: 200 kDa

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Component #1: protein, Low-pH-induced dimer of human sSortilin extracellular domain

ProteinName: Low-pH-induced dimer of human sSortilin extracellular domain
Recombinant expression: No
MassExperimental: 200 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.01 mg/ml / pH: 5.5
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: 55967
3D reconstructionSoftware: RELION / Resolution: 13 Å / Resolution method: FSC 0.143 CUT-OFF

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