4Y61 | pdb_00004y61

Crystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1

• PDB DOI: https://doi.org/10.2210/pdb4Y61/pdb

• Classification: HYDROLASE/SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-02-12 Released: 2015-06-03 
• Deposition Author(s): Yamgata, A., Sato, Y., Goto-Ito, S., Uemura, T., Maeda, A., Shiroshima, T., Yoshida, T., Fukai, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.36 Å
• R-Value Free: 
  0.286 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Models: experimental

Literature

Structure of Slitrk2-PTP delta complex reveals mechanisms for splicing-dependent trans-synaptic adhesion.

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

(2015) Sci Rep 5: 9686-9686

• PubMed: 25989451 
• DOI: https://doi.org/10.1038/srep09686
• Primary Citation Related Structures: 
  4Y61


• PubMed Abstract: 
  

  Selective binding between pre- and postsynaptic adhesion molecules can induce synaptic differentiation. Here we report the crystal structure of a synaptogenic trans-synaptic adhesion complex between Slit and Trk-like family member 2 (Slitrk2) and receptor protein tyrosine phosphatase (RPTP) δ. The structure and site-directed mutational analysis revealed the structural basis of splicing-dependent adhesion between Slitrks and type IIa RPTPs for inducing synaptic differentiation.

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Organizational Affiliation: 
• 1] Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan [2] Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8501, Japan [3] CREST, JST, Saitama 332-0012, Japan.
1] Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan [2] CREST, JST, Saitama 332-0012, Japan.
1] CREST, JST, Saitama 332-0012, Japan [2] Department of Molecular and Cellular Physiology, Shinshu University School of Medicine, Nagano 390-8621, Japan [3] Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano 390-8621, Japan.
1] Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan [2] PRESTO, JST, Saitama 332-0012, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.79 kDa 
• Atom Count: 4,947 
• Modeled Residue Count: 626 
• Deposited Residue Count: 670 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase delta	A	398	Mus musculus	Mutation(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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q64487-4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SLIT and NTRK-like protein 2	B	272	Mus musculus	Mutation(s): 0  Gene Names: Slitrk2
UniProt & NIH Common Fund Data Resources
Find proteins for Q810C0 (Mus musculus) Explore Q810C0  Go to UniProtKB:  Q810C0
IMPC:  MGI:2679449
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q810C0-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth B], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.36 Å
• R-Value Free:  0.286 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.227	α = 90
b = 91.308	β = 90
c = 123.389	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Yamgata, A., Sato, Y., Goto-Ito, S., Uemura, T., Maeda, A., Shiroshima, T., Yoshida, T., Fukai, S.

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Funding Organization	Location	Grant Number
	Japan	--

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary