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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.36 Å
R-Value Free:
0.286 (Depositor), 0.290 (DCC)
R-Value Work:
0.235 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

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

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/srep09686
Primary Citation of 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.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q64487
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: Q64487-4
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q810C0
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B	Go to GlyGen: Q810C0-1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.36 Å
R-Value Free: 0.286 (Depositor), 0.290 (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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
	Japan	--

Revision History (Full details and data files)

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