5XWT

Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.178 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.

Goto-Ito, S.Yamagata, A.Sato, Y.Uemura, T.Shiroshima, T.Maeda, A.Imai, A.Mori, H.Yoshida, T.Fukai, S.

(2018) Nat Commun 9: 269-269

  • DOI: 10.1038/s41467-017-02417-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Synapse formation is triggered by trans-synaptic interactions of cell adhesion molecules, termed synaptic organizers. Three members of type-II receptor protein tyrosine phosphatases (classified as type-IIa RPTPs; PTPδ, PTPσ and LAR) are known as pres ...

    Synapse formation is triggered by trans-synaptic interactions of cell adhesion molecules, termed synaptic organizers. Three members of type-II receptor protein tyrosine phosphatases (classified as type-IIa RPTPs; PTPδ, PTPσ and LAR) are known as presynaptic organizers. Synaptic adhesion-like molecules (SALMs) have recently emerged as a family of postsynaptic organizers. Although all five SALM isoforms can bind to the type-IIa RPTPs, only SALM3 and SALM5 reportedly have synaptogenic activities depending on their binding. Here, we report the crystal structures of apo-SALM5, and PTPδ-SALM2 and PTPδ-SALM5 complexes. The leucine-rich repeat (LRR) domains of SALMs interact with the second immunoglobulin-like (Ig) domain of PTPδ, whereas the Ig domains of SALMs interact with both the second and third Ig domains of PTPδ. Unexpectedly, the structures exhibit the LRR-mediated 2:2 complex. Our synaptogenic co-culture assay using site-directed SALM5 mutants demonstrates that presynaptic differentiation induced by PTPδ-SALM5 requires the dimeric property of SALM5.


    Organizational Affiliation

    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan.,Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Nagano, 390-8621, Japan.,Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan. toyoshid@med.u-toyama.ac.jp.,Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, 930-0194, Japan.,Department of Biological Sciences for Intractable Neurological Diseases, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano, 390-8621, Japan.,CREST, JST, Saitama, 332-0012, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan. fukai@iam.u-tokyo.ac.jp.,PRESTO, JST, Saitama, 332-0012, Japan. toyoshid@med.u-toyama.ac.jp.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. fukai@iam.u-tokyo.ac.jp.,Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. fukai@iam.u-tokyo.ac.jp.,CREST, JST, Saitama, 332-0012, Japan. fukai@iam.u-tokyo.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein phosphatase delta
A, C
402Mus 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
Leucine-rich repeat and fibronectin type-III domain-containing protein 5
B, D
367Homo sapiensMutation(s): 0 
Gene Names: LRFN5 (C14orf146, SALM5)
Find proteins for Q96NI6 (Homo sapiens)
Go to Gene View: LRFN5
Go to UniProtKB:  Q96NI6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.178 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.260α = 90.00
b = 169.753β = 90.00
c = 210.946γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release