4YH7

Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.4 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.290 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.

Yamagata, A., Yoshida, T., Sato, Y., Goto-Ito, S., Uemura, T., Maeda, A., Shiroshima, T., Iwasawa-Okamoto, S., Mori, H., Mishina, M., Fukai, S.

(2015) Nat Commun 6: 6926-6926

  • DOI: 10.1038/ncomms7926
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Synapse formation is triggered through trans-synaptic interaction between pairs of pre- and postsynaptic adhesion molecules, the specificity of which depends on splice inserts known as 'splice-insert signaling codes'. Receptor protein tyrosine phosph ...

    Synapse formation is triggered through trans-synaptic interaction between pairs of pre- and postsynaptic adhesion molecules, the specificity of which depends on splice inserts known as 'splice-insert signaling codes'. Receptor protein tyrosine phosphatase δ (PTPδ) can bidirectionally induce pre- and postsynaptic differentiation of neurons by trans-synaptically binding to interleukin-1 receptor accessory protein (IL-1RAcP) and IL-1RAcP-like-1 (IL1RAPL1) in a splicing-dependent manner. Here, we report crystal structures of PTPδ in complex with IL1RAPL1 and IL-1RAcP. The first immunoglobulin-like (Ig) domain of IL1RAPL1 directly recognizes the first splice insert, which is critical for binding to IL1RAPL1. The second splice insert functions as an adjustable linker that positions the Ig2 and Ig3 domains of PTPδ for simultaneously interacting with the Ig1 domain of IL1RAPL1 or IL-1RAcP. We further identified the IL1RAPL1-specific interaction, which appears coupled to the first-splice-insert-mediated interaction. Our results thus reveal the decoding mechanism of splice-insert signaling codes for synaptic differentiation induced by trans-synaptic adhesion between PTPδ and IL1RAPL1/IL-1RAcP.

    Organizational Affiliation: 

    1] Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan [2] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8501, Japan [3] CREST, JST, Saitama 332-0012, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein phosphatase delta
A
841Mus musculusMutation(s): 0 
Gene Names: Ptprd
EC: 3.1.3.48
Find proteins for Q64487 (Mus musculus)
Go to UniProtKB:  Q64487
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor accessory protein-like 1
B
348Mus musculusMutation(s): 0 
Gene Names: Il1rapl1
Find proteins for P59823 (Mus musculus)
Go to UniProtKB:  P59823
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN
Download SDF File 
Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.4 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.290 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 286.295α = 90.00
b = 286.295β = 90.00
c = 70.183γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
HKL-2000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release