4RCA

Crystal structure of human PTPdelta and human Slitrk1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9908 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.263 

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
Receptor-type tyrosine-protein phosphatase delta
A
308Homo sapiensMutation(s): 0 
Gene Names: PTPRD
EC: 3.1.3.48
Find proteins for P23468 (Homo sapiens)
Go to Gene View: PTPRD
Go to UniProtKB:  P23468
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SLIT and NTRK-like protein 1
B
251Homo sapiensMutation(s): 0 
Gene Names: SLITRK1 (KIAA1910, LRRC12)
Find proteins for Q96PX8 (Homo sapiens)
Go to Gene View: SLITRK1
Go to UniProtKB:  Q96PX8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
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: 2.9908 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.981α = 90.00
b = 60.195β = 102.19
c = 83.679γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
PHENIXmodel building
REFMACrefinement
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