5WY8

Crystal structure of PTP delta Ig1-Ig3 in complex with IL1RAPL1 Ig1-Ig3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

LAR-RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate

Won, S.Y.Kim, C.Y.Kim, D.Ko, J.Um, J.W.Lee, S.B.Buck, M.Kim, E.Heo, W.D.Lee, J.O.Kim, H.M.

(2017) Front Mol Neurosci 10: 327-327

  • DOI: 10.3389/fnmol.2017.00327

  • PubMed Abstract: 
  • The leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs) are cellular receptors of heparan sulfate (HS) and chondroitin sulfate (CS) proteoglycans that direct axonal growth and neuronal regeneration. LAR-RPTPs are also ...

    The leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs) are cellular receptors of heparan sulfate (HS) and chondroitin sulfate (CS) proteoglycans that direct axonal growth and neuronal regeneration. LAR-RPTPs are also synaptic adhesion molecules that form trans -synaptic adhesion complexes by binding to various postsynaptic adhesion ligands, such as Slit- and Trk-like family of proteins (Slitrks), IL-1 receptor accessory protein-like 1 (IL1RAPL1), interleukin-1 receptor accessory protein (IL-1RAcP) and neurotrophin receptor tyrosine kinase C (TrkC), to regulate synaptogenesis. Here, we determined the crystal structure of the human LAR-RPTP/IL1RAPL1 complex and found that lateral interactions between neighboring LAR-RPTP/IL1RAPL1 complexes in crystal lattices are critical for the higher-order assembly and synaptogenic activity of these complexes. Moreover, we found that LAR-RPTP binding to the postsynaptic adhesion ligands, Slitrk3, IL1RAPL1 and IL-1RAcP, but not TrkC, induces reciprocal higher-order clustering of trans -synaptic adhesion complexes. Although LAR-RPTP clustering was induced by either HS or postsynaptic adhesion ligands, the dominant binding of HS to the LAR-RPTP was capable of dismantling pre-established LAR-RPTP-mediated trans -synaptic adhesion complexes. These findings collectively suggest that LAR-RPTP clustering for synaptogenesis is modulated by a complex synapse-organizing protein network.


    Organizational Affiliation

    Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, South Korea.,Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea.,Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, OH, United States.,Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein phosphatase delta
A
298Homo 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
Interleukin-1 receptor accessory protein-like 1
B
323Homo sapiensMutation(s): 0 
Gene Names: IL1RAPL1 (OPHN4)
Find proteins for Q9NZN1 (Homo sapiens)
Go to Gene View: IL1RAPL1
Go to UniProtKB:  Q9NZN1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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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: 3.07 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.233 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 110.416α = 90.00
b = 110.416β = 90.00
c = 210.536γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NRFKorea, Republic OfNRF-2015R1A2A2A01005533

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release