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- PDB-4yh7: Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1 -

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Basic information

Entry
Database: PDB / ID: 4yh7
TitleCrystal structure of PTPdelta ectodomain in complex with IL1RAPL1
Components
  • Interleukin-1 receptor accessory protein-like 1
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsHYDROLASE/IMMUNE SYSTEM / Trans-synaptic complex / Synapse organizer / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Interleukin-38 signaling / 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 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase ...Interleukin-38 signaling / 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 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of dendrite morphogenesis / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of synapse assembly / negative regulation of exocytosis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / 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 / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / cellular response to hypoxia / postsynaptic membrane / axon / signaling receptor binding / dendrite / glutamatergic synapse / cell surface / signal transduction / plasma membrane / cytoplasm
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / : / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / : / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin / Immunoglobulin domain / 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 / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / 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
Interleukin-1 receptor accessory protein-like 1 / Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å
AuthorsYamagata, A. / Fukai, S.
CitationJournal: Nat Commun / Year: 2015
Title: Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Authors: Yamagata, A. / Yoshida, T. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Iwasawa-Okamoto, S. / Mori, H. / Mishina, M. / Fukai, S.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site ..._chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / exptl_crystal / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _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 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Interleukin-1 receptor accessory protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1536
Polymers133,3762
Non-polymers1,7784
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint14 kcal/mol
Surface area50150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)286.295, 286.295, 70.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 93559.461 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-854
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase
#2: Protein Interleukin-1 receptor accessory protein-like 1 / IL1RAPL-1 / X-linked interleukin-1 receptor accessory protein-like 1


Mass: 39816.277 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il1rapl1 / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: P59823
#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.: 1
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 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}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.: 2
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
Sequence detailsSEQUENCE OF THE CHAIN A WAS BASED ON ISOFORM 12 OF DATABASE UNP Q64487

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.39 Å3/Da / Density % sol: 77.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15% PEG4000, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.4→50 Å / Num. obs: 17618 / % possible obs: 95.6 % / Redundancy: 4.2 % / Rsym value: 0.072 / Net I/σ(I): 17.7
Reflection shellResolution: 4.4→4.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.2 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YFC, 2DJU, 2DLH

4yfc
PDB Unreleased entry

2dju

2dlh


Resolution: 4.4→39.09 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 37.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3246 896 5.09 %
Rwork0.2904 --
obs0.292 17614 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.4→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7123 0 117 0 7240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067414
X-RAY DIFFRACTIONf_angle_d1.57510078
X-RAY DIFFRACTIONf_dihedral_angle_d19.8312810
X-RAY DIFFRACTIONf_chiral_restr0.0641141
X-RAY DIFFRACTIONf_plane_restr0.0081297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3996-4.67480.35661290.33242526X-RAY DIFFRACTION87
4.6748-5.0350.33071690.29372660X-RAY DIFFRACTION93
5.035-5.54050.31651640.27912780X-RAY DIFFRACTION97
5.5405-6.33920.32341370.26762853X-RAY DIFFRACTION97
6.3392-7.97560.33021490.31522907X-RAY DIFFRACTION99
7.9756-39.09170.31851480.28212992X-RAY DIFFRACTION99

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