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- PDB-5xwu: Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig -

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Basic information

Entry
Database: PDB / ID: 5xwu
TitleCrystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig
Components
  • Leucine-rich repeat and fibronectin type III domain-containing protein 1
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsCELL ADHESION / synaptic orgnizers
Function / homology
Function and homology information


: / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / synaptic membrane adhesion / regulation of postsynaptic density assembly / presynapse assembly / negative regulation of receptor signaling pathway via JAK-STAT ...: / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / synaptic membrane adhesion / regulation of postsynaptic density assembly / presynapse assembly / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of immune response / dephosphorylation / hippocampal mossy fiber to CA3 synapse / cell adhesion molecule binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / signaling receptor binding / glutamatergic synapse / cell surface
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Leucine-rich repeat profile. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Leucine-rich repeat / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Leucine-rich repeat domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Leucine-rich repeat and fibronectin type III domain-containing protein 1 / Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.162 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 / 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_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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 1
C: Receptor-type tyrosine-protein phosphatase delta
D: Leucine-rich repeat and fibronectin type III domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,92413
Polymers149,3764
Non-polymers2,5499
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint19 kcal/mol
Surface area63680 Å2
Unit cell
Length a, b, c (Å)90.040, 127.198, 210.919
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: 34432.973 Da / Num. of mol.: 2 / Fragment: UNP residues 20-321
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 1 / Synaptic adhesion-like molecule 2 / Synaptic differentiation-enhancing molecule 1


Mass: 40254.949 Da / Num. of mol.: 2 / Fragment: UNP residues 32-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrfn1, Salm2, Semo1 / Production host: Homo sapiens (human) / References: UniProt: Q2WF71
#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.: 3
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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM

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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: 4.04 Å3/Da / Density % sol: 69.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 7% PEG 20000, 0.1M MES (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 41658 / % possible obs: 99.8 % / Redundancy: 9.6 % / Net I/σ(I): 7.48

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.162→48.71 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 2029 4.88 %
Rwork0.218 --
obs0.22 41611 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.162→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9809 0 164 0 9973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310176
X-RAY DIFFRACTIONf_angle_d0.68113837
X-RAY DIFFRACTIONf_dihedral_angle_d10.7773761
X-RAY DIFFRACTIONf_chiral_restr0.0271626
X-RAY DIFFRACTIONf_plane_restr0.0031817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1619-3.2410.36221150.32422363X-RAY DIFFRACTION83
3.241-3.32860.36591460.29112819X-RAY DIFFRACTION100
3.3286-3.42650.30591350.26642821X-RAY DIFFRACTION100
3.4265-3.5370.30511660.26352801X-RAY DIFFRACTION100
3.537-3.66340.30521490.24282801X-RAY DIFFRACTION100
3.6634-3.810.28781390.2292855X-RAY DIFFRACTION100
3.81-3.98340.26451400.21982842X-RAY DIFFRACTION100
3.9834-4.19330.26391590.21032814X-RAY DIFFRACTION100
4.1933-4.45580.24831300.18142890X-RAY DIFFRACTION100
4.4558-4.79960.18361430.16992848X-RAY DIFFRACTION100
4.7996-5.28210.22351510.17912870X-RAY DIFFRACTION100
5.2821-6.04520.22681490.20282901X-RAY DIFFRACTION100
6.0452-7.61160.24061340.21472939X-RAY DIFFRACTION100
7.6116-48.71590.23411730.2073018X-RAY DIFFRACTION99

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