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- PDB-5xnp: Crystal structures of human SALM5 in complex with human PTPdelta -

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Basic information

Entry
Database: PDB / ID: 5xnp
TitleCrystal structures of human SALM5 in complex with human PTPdelta
Components
  • Leucine-rich repeat and fibronectin type-III domain-containing protein 5
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsMEMBRANE PROTEIN/HYDROLASE / Regulating some neural developments / MEMBRANE PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / negative regulation of macrophage activation / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / Synaptic adhesion-like molecules ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / negative regulation of macrophage activation / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / Synaptic adhesion-like molecules / negative regulation of receptor signaling pathway via JAK-STAT / phosphate-containing compound metabolic process / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of presynapse assembly / regulation of immune response / GABA-ergic synapse / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / neuron differentiation / negative regulation of inflammatory response / presynaptic membrane / receptor complex / signaling receptor binding / glutamatergic synapse / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / BspA type Leucine rich repeat region (6 copies) / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / BspA type Leucine rich repeat region (6 copies) / Immunoglobulin domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / 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
Receptor-type tyrosine-protein phosphatase delta / Leucine-rich repeat and fibronectin type-III domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.729 Å
AuthorsLiu, H. / Lin, Z. / Xu, F.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of SALM5-induced PTP delta dimerization for synaptic differentiation
Authors: Lin, Z. / Liu, J. / Ding, H. / Xu, F. / Liu, H.
History
DepositionMay 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
B: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
D: Receptor-type tyrosine-protein phosphatase delta
E: Receptor-type tyrosine-protein phosphatase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,13642
Polymers145,0294
Non-polymers3,10638
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-182 kcal/mol
Surface area64920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.384, 249.384, 249.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Protein , 2 types, 4 molecules ABDE

#1: Protein Leucine-rich repeat and fibronectin type-III domain-containing protein 5


Mass: 40468.383 Da / Num. of mol.: 2 / Fragment: UNP residues 18-374
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
#2: Protein Receptor-type tyrosine-protein phosphatase delta / R-PTP-delta


Mass: 32046.260 Da / Num. of mol.: 2 / Fragment: UNP residues 21-320 / Mutation: 181-189 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRD / Production host: Homo sapiens (human) / References: UniProt: P23468, protein-tyrosine-phosphatase

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Sugars , 1 types, 8 molecules

#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.: 8
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

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Non-polymers , 5 types, 124 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 4.46 Å3/Da / Density % sol: 72.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Tartrate Na/K, MES pH 6.0, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.729→50 Å / Num. obs: 26924 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.109 / Χ2: 1.563 / Net I/σ(I): 18.75
Reflection shellResolution: 3.729→3.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1340 / CC1/2: 0.727 / Χ2: 1.656 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XNQ, 4YH7

5xnq

4yh7


Resolution: 3.729→48.908 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.44
RfactorNum. reflection% reflection
Rfree0.2638 1316 4.92 %
Rwork0.2316 --
obs0.2332 26749 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.729→48.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10166 0 158 94 10418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310526
X-RAY DIFFRACTIONf_angle_d0.73914352
X-RAY DIFFRACTIONf_dihedral_angle_d12.3856476
X-RAY DIFFRACTIONf_chiral_restr0.0471680
X-RAY DIFFRACTIONf_plane_restr0.0041868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7292-3.87850.30971230.29742835X-RAY DIFFRACTION100
3.8785-4.05490.35971480.29062796X-RAY DIFFRACTION99
4.0549-4.26860.26771440.26422813X-RAY DIFFRACTION99
4.2686-4.53580.25561530.23032821X-RAY DIFFRACTION100
4.5358-4.88580.22631440.21392841X-RAY DIFFRACTION100
4.8858-5.37690.27511500.22022808X-RAY DIFFRACTION100
5.3769-6.15360.27691540.24052821X-RAY DIFFRACTION99
6.1536-7.74790.29621590.22892845X-RAY DIFFRACTION100
7.7479-48.91240.21761410.20752853X-RAY DIFFRACTION96

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