[English] 日本語
Yorodumi
- PDB-4yfd: Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yfd
TitleCrystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP
Components
  • Interleukin-1 receptor accessory protein
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsIMMUNE SYSTEM/HYDROLASE / trans-synaptic complex / synapse organizer / IMMUNE SYSTEM-HYDROLASE complex
Function / homology
Function and homology information


Interleukin-33 signaling / Interleukin-36 pathway / interleukin-33 receptor activity / trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / interleukin-1 receptor activity / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / PIP3 activates AKT signaling ...Interleukin-33 signaling / Interleukin-36 pathway / interleukin-33 receptor activity / trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / interleukin-1 receptor activity / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / PIP3 activates AKT signaling / Interleukin-1 signaling / synaptic membrane adhesion / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / interleukin-33-mediated signaling pathway / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / 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 / interleukin-1-mediated signaling pathway / heterophilic cell-cell adhesion / positive regulation of interleukin-4 production / regulation of presynapse assembly / regulation of immune response / coreceptor activity / cell adhesion molecule binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein tyrosine kinase binding / hippocampal mossy fiber to CA3 synapse / positive regulation of NF-kappaB transcription factor activity / modulation of chemical synaptic transmission / positive regulation of interleukin-6 production / Schaffer collateral - CA1 synapse / neuron differentiation / cytokine-mediated signaling pathway / presynaptic membrane / inflammatory response / signaling receptor binding / innate immune response / synapse / glutamatergic synapse / extracellular region / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / : / TIR domain / Immunoglobulin domain / Toll - interleukin 1 - resistance / TIR domain profile. ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / : / TIR domain / Immunoglobulin domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / 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 / Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.253 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 25, 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_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_oper_list.symmetry_operation
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 / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Interleukin-1 receptor accessory protein
A: Receptor-type tyrosine-protein phosphatase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8299
Polymers93,2812
Non-polymers1,5487
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint12 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.497, 63.306, 169.350
Angle α, β, γ (deg.)90.00, 94.23, 90.00
Int Tables number3
Space group name H-MP121

-
Components

#1: Protein Interleukin-1 receptor accessory protein / IL-1RAcP


Mass: 39368.535 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il1rap / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q61730
#2: Protein Receptor-type tyrosine-protein phosphatase delta / R-PTP-delta


Mass: 53912.441 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-511
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
#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.: 7
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.34 Å3/Da / Density % sol: 71.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% PEG3350, 0.1 M ammonium sulfate and 0.1 M tri-sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 25436 / % possible obs: 97.3 % / Redundancy: 4.7 % / Rsym value: 0.118 / Net I/σ(I): 10.7
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2 / % possible all: 92.5

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YD6, 2YD9, 4DEP, 3O4O, 4YFE

2yd6

2yd9

4dep

3o4o

4yfe


Resolution: 3.253→48.974 Å / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 33.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2867 1292 5.08 %
Rwork0.2558 --
obs0.2574 25418 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.253→48.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6505 0 0 0 6505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056676
X-RAY DIFFRACTIONf_angle_d1.1499104
X-RAY DIFFRACTIONf_dihedral_angle_d17.1312485
X-RAY DIFFRACTIONf_chiral_restr0.0481037
X-RAY DIFFRACTIONf_plane_restr0.0061186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2525-3.38270.41681120.38722540X-RAY DIFFRACTION92
3.3827-3.53660.37131532597X-RAY DIFFRACTION94
3.5366-3.7230.3861370.32392581X-RAY DIFFRACTION95
3.723-3.95620.29981430.28522653X-RAY DIFFRACTION97
3.9562-4.26150.28231420.23372678X-RAY DIFFRACTION98
4.2615-4.690.24151460.20352707X-RAY DIFFRACTION99
4.69-5.3680.22761370.18932759X-RAY DIFFRACTION99
5.368-6.76020.27051580.24762765X-RAY DIFFRACTION99
6.7602-48.97920.26441640.23932846X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.6804 Å / Origin y: 14.5936 Å / Origin z: 31.1471 Å
111213212223313233
T0.5213 Å2-0.1218 Å2-0.0017 Å2-0.2613 Å2-0.0353 Å2--0.5726 Å2
L0.9261 °2-0.2226 °2-0.2828 °2-0.2729 °20.3176 °2--0.1207 °2
S0.0439 Å °0.0365 Å °-0.1008 Å °-0.0589 Å °0.108 Å °-0.0725 Å °-0.2196 Å °0.0344 Å °-0.127 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