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- PDB-5xwt: Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig -

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Basic information

Entry
Database: PDB / ID: 5xwt
TitleCrystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig
Components
  • Leucine-rich repeat and fibronectin type-III domain-containing protein 5
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsCELL ADHESION / synaptic orgnizers
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 / negative regulation of macrophage activation / 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 ...trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / negative regulation of macrophage activation / 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 / hippocampal mossy fiber to CA3 synapse / GABA-ergic synapse / modulation of chemical synaptic transmission / postsynaptic density membrane / Schaffer collateral - CA1 synapse / negative regulation of inflammatory response / neuron differentiation / presynaptic membrane / cellular response to hypoxia / signaling receptor binding / glutamatergic synapse / cell surface
Similarity search - Function
: / Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / BspA type Leucine rich repeat region (6 copies) / : / 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 ...: / Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / BspA type Leucine rich repeat region (6 copies) / : / 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 / Leucine-rich repeat / Fibronectin type 3 domain / 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
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Receptor-type tyrosine-protein phosphatase delta / Leucine-rich repeat and fibronectin type-III domain-containing protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.178 Å
AuthorsGoto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.
Authors: Goto-Ito, S. / Yamagata, A. / Sato, Y. / Uemura, T. / Shiroshima, T. / Maeda, A. / Imai, A. / Mori, H. / Yoshida, T. / Fukai, S.
History
DepositionJun 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
C: Receptor-type tyrosine-protein phosphatase delta
D: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,58114
Polymers170,9464
Non-polymers3,63410
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint16 kcal/mol
Surface area76700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.260, 169.753, 210.946
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: 44089.613 Da / Num. of mol.: 2 / Fragment: UNP residues 20-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase
#2: Protein Leucine-rich repeat and fibronectin type-III domain-containing protein 5


Mass: 41383.496 Da / Num. of mol.: 2 / Fragment: UNP residues 18-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRFN5, C14orf146, SALM5 / Production host: Homo sapiens (human) / References: UniProt: Q96NI6
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...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 / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#5: 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: isolated from a genetically manipulated source
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: 5.15 Å3/Da / Density % sol: 76.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 7% PEG 4000, 0.1M NaCl, 0.1M Li2SO4, 0.1M ADA (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.94→50 Å / Num. obs: 31657 / % possible obs: 99.2 % / Redundancy: 10.9 % / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 4.178→49.862 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 30.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3113 1252 4.89 %
Rwork0.2608 --
obs0.2633 25606 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.178→49.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11289 0 238 0 11527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211796
X-RAY DIFFRACTIONf_angle_d0.616088
X-RAY DIFFRACTIONf_dihedral_angle_d9.6994331
X-RAY DIFFRACTIONf_chiral_restr0.0231905
X-RAY DIFFRACTIONf_plane_restr0.0032088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1776-4.34470.37611220.31082222X-RAY DIFFRACTION80
4.3447-4.54240.34151150.28762697X-RAY DIFFRACTION96
4.5424-4.78170.28531310.27722714X-RAY DIFFRACTION97
4.7817-5.0810.32381480.27272691X-RAY DIFFRACTION97
5.081-5.47280.2861440.26232739X-RAY DIFFRACTION97
5.4728-6.02270.35341530.26832728X-RAY DIFFRACTION97
6.0227-6.89230.30831480.26132779X-RAY DIFFRACTION98
6.8923-8.67610.30991460.24262818X-RAY DIFFRACTION98
8.6761-49.86550.28021450.23092966X-RAY DIFFRACTION98

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