4RCA

Crystal structure of human PTPdelta and human Slitrk1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/ncomms6423
  • Primary Citation of Related Structures:  
    4RCA, 4RCW

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase delta308Homo sapiensMutation(s): 0 
Gene Names: PTPRD
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P23468 (Homo sapiens)
Explore P23468 
Go to UniProtKB:  P23468
PHAROS:  P23468
GTEx:  ENSG00000153707 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23468
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P23468-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SLIT and NTRK-like protein 1251Homo sapiensMutation(s): 0 
Gene Names: SLITRK1KIAA1910LRRC12UNQ233/PRO266
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PX8 (Homo sapiens)
Explore Q96PX8 
Go to UniProtKB:  Q96PX8
PHAROS:  Q96PX8
GTEx:  ENSG00000178235 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96PX8
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q96PX8-1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.981α = 90
b = 60.195β = 102.19
c = 83.679γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
HKL-2000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary