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- PDB-5y32: Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1 -

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Basic information

Entry
Database: PDB / ID: 5y32
TitleCrystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1
Components
  • Interleukin-1 receptor accessory protein-like 1
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsIMMUNE SYSTEM/HYDROLASE / TRANS-SYNAPTIC / ADHESION COMPLEX / IMMUNE SYSTEM-HYDROLASE 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 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / regulation of postsynaptic density assembly ...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 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / regulation of postsynaptic density assembly / 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 / heterophilic cell-cell adhesion / negative regulation of exocytosis / regulation of neuron projection development / regulation of immune response / cell adhesion molecule binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampal mossy fiber to CA3 synapse / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / postsynaptic membrane / signaling receptor binding / axon / 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 profile. / Tyrosine-specific protein phosphatases domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.701 Å
AuthorsYamagata, A. / Fukai, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSTCREST Japan
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
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 16, 2017ID: 4YFC
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _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 22, 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 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
B: Interleukin-1 receptor accessory protein-like 1
A: Receptor-type tyrosine-protein phosphatase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4757
Polymers73,3052
Non-polymers2,1705
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SPR measurement
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint33 kcal/mol
Surface area28760 Å2
Unit cell
Length a, b, c (Å)162.975, 81.175, 91.480
Angle α, β, γ (deg.)90.00, 91.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein Interleukin-1 receptor accessory protein-like 1 / IL1RAPL-1 / X-linked interleukin-1 receptor accessory protein-like 1


Mass: 39617.070 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 / Production host: Homo sapiens (human) / References: UniProt: P59823
#2: Protein Receptor-type tyrosine-protein phosphatase delta / R-PTP-delta


Mass: 33688.012 Da / Num. of mol.: 1 / Fragment: UNP residues 21-318
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

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Sugars , 4 types, 5 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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

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Non-polymers , 1 types, 77 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15% PEG4 000, 0.1 M 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: RAYONIX MX-225 / Detector: CCD / Date: Mar 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 32256 / % possible obs: 98.7 % / Redundancy: 5.1 % / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 3.2 / % possible all: 95.9

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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, 4DEP, 3O4O

2yd6

4dep

3o4o


Resolution: 2.701→45.729 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 29.3
RfactorNum. reflection% reflection
Rfree0.2573 1638 5.08 %
Rwork0.2137 --
obs0.2159 32242 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.701→45.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 143 77 4428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074454
X-RAY DIFFRACTIONf_angle_d1.2626036
X-RAY DIFFRACTIONf_dihedral_angle_d15.8421688
X-RAY DIFFRACTIONf_chiral_restr0.069693
X-RAY DIFFRACTIONf_plane_restr0.005766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7014-2.78090.41471350.36932254X-RAY DIFFRACTION87
2.7809-2.87070.3511250.33342484X-RAY DIFFRACTION97
2.8707-2.97330.32241180.30712551X-RAY DIFFRACTION98
2.9733-3.09230.32221320.28092514X-RAY DIFFRACTION98
3.0923-3.2330.31711410.26262585X-RAY DIFFRACTION99
3.233-3.40340.26411420.23692568X-RAY DIFFRACTION99
3.4034-3.61650.27951280.21452574X-RAY DIFFRACTION99
3.6165-3.89560.22071250.20152608X-RAY DIFFRACTION100
3.8956-4.28740.20651400.16182600X-RAY DIFFRACTION100
4.2874-4.90720.19541350.13612599X-RAY DIFFRACTION100
4.9072-6.18010.20871510.16942613X-RAY DIFFRACTION100
6.1801-45.73530.25221660.19832654X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -51.2714 Å / Origin y: -10.8237 Å / Origin z: 19.7707 Å
111213212223313233
T0.2403 Å2-0.0088 Å20.0103 Å2-0.2472 Å2-0.0079 Å2--0.2366 Å2
L0.7296 °2-0.2952 °20.5241 °2-1.5015 °2-0.1288 °2--1.3732 °2
S0.0258 Å °0.0519 Å °0.0008 Å °0.3013 Å °-0.0474 Å °-0.2209 Å °-0.0225 Å °0.1303 Å °-0.0048 Å °
Refinement TLS groupSelection details: all

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