4PBV

Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural basis for extracellular cis and trans RPTP sigma signal competition in synaptogenesis.

Coles, C.H.Mitakidis, N.Zhang, P.Elegheert, J.Lu, W.Stoker, A.W.Nakagawa, T.Craig, A.M.Jones, E.Y.Aricescu, A.R.

(2014) Nat Commun 5: 5209-5209

  • DOI: 10.1038/ncomms6209
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Receptor protein tyrosine phosphatase sigma (RPTPσ) regulates neuronal extension and acts as a presynaptic nexus for multiple protein and proteoglycan interactions during synaptogenesis. Unknown mechanisms govern the shift in RPTPσ function, from out ...

    Receptor protein tyrosine phosphatase sigma (RPTPσ) regulates neuronal extension and acts as a presynaptic nexus for multiple protein and proteoglycan interactions during synaptogenesis. Unknown mechanisms govern the shift in RPTPσ function, from outgrowth promotion to synaptic organization. Here, we report crystallographic, electron microscopic and small-angle X-ray scattering analyses, which reveal sufficient inter-domain flexibility in the RPTPσ extracellular region for interaction with both cis (same cell) and trans (opposite cell) ligands. Crystal structures of RPTPσ bound to its postsynaptic ligand TrkC detail an interaction surface partially overlapping the glycosaminoglycan-binding site. Accordingly, heparan sulphate and heparin oligomers compete with TrkC for RPTPσ binding in vitro and disrupt TrkC-dependent synaptic differentiation in neuronal co-culture assays. We propose that transient RPTPσ ectodomain emergence from the presynaptic proteoglycan layer allows capture by TrkC to form a trans-synaptic complex, the consequent reduction in RPTPσ flexibility potentiating interactions with additional ligands to orchestrate excitatory synapse formation.


    Organizational Affiliation

    Brain Research Centre and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada V6T 2B5.,Cancer Section, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK.,Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, 702 Light Hall (0615), Nashville, Tennessee 37232-0615, USA.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NT-3 growth factor receptor
A, B
268Gallus gallusMutation(s): 5 
Gene Names: NTRK3 (TRKC)
EC: 2.7.10.1
Find proteins for Q91044 (Gallus gallus)
Go to Gene View: NTRK3
Go to UniProtKB:  Q91044
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein-tyrosine phosphatase CRYPalpha1 isoform
C, D, E
299Gallus gallusMutation(s): 0 
Gene Names: PTPRS
EC: 3.1.3.48
Find proteins for F1NWE3 (Gallus gallus)
Go to Gene View: PTPRS
Go to UniProtKB:  F1NWE3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.300α = 90.00
b = 122.160β = 109.79
c = 98.610γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG0700232
Medical Research Council (United Kingdom)United KingdomG9900061
Cancer Research UKUnited KingdomA10976
Wellcome TrustUnited Kingdom090532/Z/09/Z
Wellcome TrustUnited KingdomDPhil Studentship for N.M.

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-11-19
    Type: Database references
  • Version 2.0: 2017-08-30
    Type: Atomic model, Author supporting evidence, Derived calculations