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- PDB-4y61: Crystal structure of the complex between Slitrk2 LRR1 and PTP del... -

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Basic information

Entry
Database: PDB / ID: 4y61
TitleCrystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1
Components
  • Receptor-type tyrosine-protein phosphatase delta
  • SLIT and NTRK-like protein 2
KeywordsHYDROLASE/SIGNALING PROTEIN / trans-synaptic complex / HYDROLASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / synaptic membrane adhesion / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of dendrite morphogenesis ...trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / synaptic membrane adhesion / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of dendrite morphogenesis / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of presynapse assembly / regulation of immune response / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / axonogenesis / hippocampal mossy fiber to CA3 synapse / GABA-ergic synapse / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / cellular response to hypoxia / postsynaptic membrane / signaling receptor binding / dendrite / glutamatergic synapse / membrane / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Immunoglobulin domain ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Leucine-rich repeat profile. / Fibronectin type III domain / Fibronectin type 3 domain / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Leucine-rich repeat domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase delta / SLIT and NTRK-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.358 Å
AuthorsYamgata, A. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Yoshida, T. / Fukai, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Sci Rep / Year: 2015
Title: Structure of Slitrk2-PTP delta complex reveals mechanisms for splicing-dependent trans-synaptic adhesion.
Authors: Yamagata, A. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Yoshida, T. / Fukai, S.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_detector / diffrn_source ...diffrn_detector / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site ..._diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase delta
B: SLIT and NTRK-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7866
Polymers74,9012
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint14 kcal/mol
Surface area32540 Å2
Unit cell
Length a, b, c (Å)87.227, 91.308, 123.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase delta / R-PTP-delta


Mass: 43772.168 Da / Num. of mol.: 1 / Fragment: UNP residues 21-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Plasmid: pEBMulti-Neo / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase
#2: Protein SLIT and NTRK-like protein 2


Mass: 31129.096 Da / Num. of mol.: 1 / Fragment: UNP residues 1-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slitrk2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q810C0
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15% PEG4000, 0.1 M sodium acetate, 0.1 M MES / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 14509 / % possible obs: 99.2 % / Redundancy: 9.5 % / Rsym value: 0.13 / Net I/σ(I): 14.3
Reflection shellResolution: 3.35→3.41 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.9 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YD6, 2YD9, 2DJU, and 1OZN

2yd6

2yd9

2dju

1ozn


Resolution: 3.358→45.654 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 30.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 728 5.03 %
Rwork0.2346 --
obs0.2373 14477 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.358→45.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4891 0 56 0 4947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055058
X-RAY DIFFRACTIONf_angle_d1.1136881
X-RAY DIFFRACTIONf_dihedral_angle_d16.1471901
X-RAY DIFFRACTIONf_chiral_restr0.04800
X-RAY DIFFRACTIONf_plane_restr0.005899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3577-3.61680.35441410.29192675X-RAY DIFFRACTION98
3.6168-3.98060.28231490.2622694X-RAY DIFFRACTION99
3.9806-4.55620.30131530.21192733X-RAY DIFFRACTION100
4.5562-5.73850.26091430.20972754X-RAY DIFFRACTION99
5.7385-45.65820.27831420.2372893X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3945-1.48511.3091.0839-0.87691.2439-0.12230.23520.1782-0.2073-0.058-0.0392-0.09720.1218-0.00180.627-0.0963-0.10870.4864-0.0290.6714-36.2835-1.7626-8.266
22.80870.14890.26412.7843-0.08731.29890.23580.04830.02530.1191-0.0450.2376-0.31720.18430.19790.3496-0.05320.0560.32950.01450.4292-25.09774.81353.3499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and (resseq 28:418 or resseq 501:502))
2X-RAY DIFFRACTION2(chain B and (resseq 29:263 or resseq 301:302))

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