Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 151.92 kDa 
• Atom Count: 9973 
• Residue Count: 1270 
• Unique protein chains: 2

5XWU

Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig

• DOI: 10.2210/pdb5XWU/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-06-30 Released: 2018-06-06 
• Deposition Author(s): Goto-Ito, S., Yamagata, A., Sato, Y., Fukai, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 0.259 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

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

• PubMed: 29348429 
• DOI: 10.1038/s41467-017-02417-z
• Primary Citation of Related Structures:  
  5XWS, 5XWU, 5XWT


• 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.

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Organizational Affiliation: 

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase delta	A, C	313	Mus musculus	Mutation(s): 0  Gene Names: Ptprd EC: 3.1.3.48
Find proteins for Q64487 (Mus musculus) Explore Q64487  Go to UniProtKB:  Q64487
NIH Common Fund Data Resources
IMPC:  MGI:97812

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat and fibronectin type III domain-containing protein 1	B, D	365	Mus musculus	Mutation(s): 0  Gene Names: Lrfn1, Salm2, Semo1
Find proteins for Q2WF71 (Mus musculus) Explore Q2WF71  Go to UniProtKB:  Q2WF71

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	A, C	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 0.259 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.04	α = 90
b = 127.198	β = 90
c = 210.919	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-06-30 
• Released Date: 2018-06-06 
Deposition Author(s): Goto-Ito, S., Yamagata, A., Sato, Y., Fukai, S.

Revision History 

• 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