4PBV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1038/ncomms6209
  • Primary Citation of Related Structures:  
    4PBV, 4PBW, 4PBX

  • 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 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

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NT-3 growth factor receptor
A, B
268Gallus gallusMutation(s): 5 
Gene Names: NTRK3TRKC
EC: 2.7.10.1
UniProt
Find proteins for Q91044 (Gallus gallus)
Explore Q91044 
Go to UniProtKB:  Q91044
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91044
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-tyrosine phosphatase CRYPalpha1 isoform
C, D, E
299Gallus gallusMutation(s): 0 
Gene Names: CRYPalpha1
UniProt
Find proteins for F1NWE3 (Gallus gallus)
Explore F1NWE3 
Go to UniProtKB:  F1NWE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1NWE3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.3α = 90
b = 122.16β = 109.79
c = 98.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 2.0: 2017-08-30
    Changes: Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary