[English] 日本語
Yorodumi
- PDB-5y32: Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1 -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...Interleukin-38 signaling / 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 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / negative regulation of exocytosis / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / regulation of postsynapse organization / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly / regulation of immune response / dephosphorylation / hippocampal mossy fiber to CA3 synapse / cell adhesion molecule binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / 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 / Immunoglobulin ...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 / 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. / 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 / Immunoglobulins / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / N-Acetylglucosamine


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

-
Non-polymers , 1 types, 77 molecules

#7: Water ChemComp-HOH / water / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more