6EHO

Dimer of the Sortilin Vps10p domain at low pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Acidic Environment Induces Dimerization and Ligand Binding Site Collapse in the Vps10p Domain of Sortilin.

Januliene, D.Andersen, J.L.Nielsen, J.A.Quistgaard, E.M.Hansen, M.Strandbygaard, D.Moeller, A.Petersen, C.M.Madsen, P.Thirup, S.S.

(2017) Structure 25: 1809-1819.e3

  • DOI: 10.1016/j.str.2017.09.015

  • PubMed 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 various acidic conditions. The crystal structure of the s ...

    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.


    Organizational Affiliation

    MIND Centre, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,MIND Centre, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark. Electronic address: sth@mbg.au.dk.,MIND Centre, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.,MIND Centre, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sortilin
A
723Homo sapiensMutation(s): 2 
Gene Names: SORT1
Find proteins for Q99523 (Homo sapiens)
Go to Gene View: SORT1
Go to UniProtKB:  Q99523
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 189.010α = 90.00
b = 189.010β = 90.00
c = 189.010γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Lundbeck FoundationDenmark--

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references