4RCW

Crystal structure of human Slitrk1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1925 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for LAR-RPTP/Slitrk complex-mediated synaptic adhesion.

Um, J.W.Kim, K.H.Park, B.S.Choi, Y.Kim, D.Kim, C.Y.Kim, S.J.Kim, M.Ko, J.S.Lee, S.G.Choii, G.Nam, J.Heo, W.D.Kim, E.Lee, J.O.Ko, J.Kim, H.M.

(2014) Nat Commun 5: 5423-5423

  • DOI: 10.1038/ncomms6423
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Synaptic adhesion molecules orchestrate synaptogenesis. The presynaptic leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs) regulate synapse development by interacting with postsynaptic Slit- and Trk-like family protei ...

    Synaptic adhesion molecules orchestrate synaptogenesis. The presynaptic leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs) regulate synapse development by interacting with postsynaptic Slit- and Trk-like family proteins (Slitrks), which harbour two extracellular leucine-rich repeats (LRR1 and LRR2). Here we identify the minimal regions of the LAR-RPTPs and Slitrks, LAR-RPTPs Ig1-3 and Slitrks LRR1, for their interaction and synaptogenic function. Subsequent crystallographic and structure-guided functional analyses reveal that the splicing inserts in LAR-RPTPs are key molecular determinants for Slitrk binding and synapse formation. Moreover, structural comparison of the two Slitrk1 LRRs reveal that unique properties on the concave surface of Slitrk1 LRR1 render its specific binding to LAR-RPTPs. Finally, we demonstrate that lateral interactions between adjacent trans-synaptic LAR-RPTPs/Slitrks complexes observed in crystal lattices are critical for Slitrk1-induced lateral assembly and synaptogenic activity. Thus, we propose a model in which Slitrks mediate synaptogenic functions through direct binding to LAR-RPTPs and the subsequent lateral assembly of LAR-RPTPs/Slitrks complexes.


    Organizational Affiliation

    Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SLIT and NTRK-like protein 1
A, B
240Homo sapiensMutation(s): 0 
Gene Names: SLITRK1 (KIAA1910, LRRC12)
Find proteins for Q96PX8 (Homo sapiens)
Go to Gene View: SLITRK1
Go to UniProtKB:  Q96PX8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1925 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.259 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.607α = 90.00
b = 69.607β = 90.00
c = 409.946γ = 120.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references