5XWT | pdb_00005xwt

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.18 Å
  • R-Value Free: 
    0.311 (Depositor), 0.318 (DCC) 
  • R-Value Work: 
    0.261 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 
    0.263 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1038/s41467-017-02417-z
  • Primary Citation Related Structures: 
    5XWS, 5XWT, 5XWU

  • 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 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
    • Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.

Macromolecule Content 

  • Total Structure Weight: 174.58 kDa 
  • Atom Count: 11,527 
  • Modeled Residue Count: 1,447 
  • Deposited Residue Count: 1,538 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase delta
A, C
402Mus musculusMutation(s): 0 
Gene Names: Ptprd
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q64487 (Mus musculus)
Explore Q64487 
Go to UniProtKB:  Q64487
IMPC:  MGI:97812
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64487
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q64487-4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeat and fibronectin type-III domain-containing protein 5
B, D
367Homo sapiensMutation(s): 0 
Gene Names: LRFN5C14orf146SALM5
UniProt & NIH Common Fund Data Resources
Find proteins for Q96NI6 (Homo sapiens)
Explore Q96NI6 
Go to UniProtKB:  Q96NI6
PHAROS:  Q96NI6
GTEx:  ENSG00000165379 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96NI6
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q96NI6-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, H, I, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G47362BJ
GlyCosmos: G47362BJ
GlyGen: G47362BJ

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.18 Å
  • R-Value Free:  0.311 (Depositor), 0.318 (DCC) 
  • R-Value Work:  0.261 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 0.263 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.26α = 90
b = 169.753β = 90
c = 210.946γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary