[English] 日本語
Yorodumi
- PDB-1irs: IRS-1 PTB DOMAIN COMPLEXED WITH A IL-4 RECEPTOR PHOSPHOPEPTIDE, N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1irs
TitleIRS-1 PTB DOMAIN COMPLEXED WITH A IL-4 RECEPTOR PHOSPHOPEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE
Components
  • IL-4 RECEPTOR PHOSPHOPEPTIDE
  • IRS-1IRS1
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/PEPTIDE) / PHOSPHOTYROSINE BINDING DOMAIN (PTB) / COMPLEX / SIGNAL TRANSDUCTION / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) complex
Function / homology
Function and homology information


interleukin-4 receptor activity / production of molecular mediator involved in inflammatory response / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / positive regulation of T-helper 2 cell differentiation / IRS-related events triggered by IGF1R / interleukin-4-mediated signaling pathway / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / positive regulation of mast cell degranulation ...interleukin-4 receptor activity / production of molecular mediator involved in inflammatory response / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / positive regulation of T-helper 2 cell differentiation / IRS-related events triggered by IGF1R / interleukin-4-mediated signaling pathway / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / positive regulation of mast cell degranulation / insulin receptor complex / positive regulation of glucose metabolic process / positive regulation of macrophage activation / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / T-helper 2 cell differentiation / Signaling by Leptin / cytokine receptor activity / PI3K/AKT activation / cellular response to fatty acid / Signaling by ALK / positive regulation of myoblast fusion / IRS activation / defense response to protozoan / immunoglobulin mediated immune response / positive regulation of immunoglobulin production / centriolar satellite / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / PI3K Cascade / negative regulation of insulin secretion / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / Growth hormone receptor signaling / positive regulation of insulin receptor signaling pathway / positive regulation of chemokine production / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor binding / Interleukin-7 signaling / SH2 domain binding / phosphotyrosine residue binding / protein kinase C binding / insulin-like growth factor receptor signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / caveola / positive regulation of glucose import / response to insulin / insulin receptor binding / cytokine-mediated signaling pathway / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / signaling receptor complex adaptor activity / glucose homeostasis / PIP3 activates AKT signaling / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / immune response / external side of plasma membrane / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / signal transduction / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Phosphotyrosine-binding domain ...Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Phosphotyrosine-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / PH-like domain superfamily / Roll / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Interleukin-4 receptor subunit alpha / Insulin receptor substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsZhou, M.-M. / Huang, B. / Olejniczak, E.T. / Meadows, R.P. / Shuker, S.B. / Miyazaki, M. / Trub, T. / Shoelson, S.E. / Feisk, S.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Structural basis for IL-4 receptor phosphopeptide recognition by the IRS-1 PTB domain.
Authors: Zhou, M.M. / Huang, B. / Olejniczak, E.T. / Meadows, R.P. / Shuker, S.B. / Miyazaki, M. / Trub, T. / Shoelson, S.E. / Fesik, S.W.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Ptb Domains of Irs-1 and Shc Have Distinct But Overlapping Binding Specificities
Authors: Wolf, G. / Trub, T. / Ottinger, E. / Groninga, L. / Lynch, A. / White, M.F. / Miyazaki, M. / Lee, J. / Shoelson, S.E.
#2: Journal: Nature / Year: 1995
Title: Structure and Ligand Recognition of the Phosphotyrosine Binding Domain of Shc
Authors: Zhou, M.M. / Ravichandran, K.S. / Olejniczak, E.F. / Petros, A.M. / Meadows, R.P. / Sattler, M. / Harlan, J.E. / Wade, W.S. / Burakoff, S.J. / Fesik, S.W.
#3: Journal: Mol.Cell.Biol. / Year: 1994
Title: Characterization of an Interaction between Insulin Receptor Substrate 1 and the Insulin Receptor by Using the Two-Hybrid System
Authors: O'Neill, T.J. / Craparo, A. / Gustafson, T.A.
History
DepositionMar 22, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IRS-1
B: IL-4 RECEPTOR PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)13,8902
Polymers13,8902
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein IRS-1 / IRS1 / INSULIN RECEPTOR SUBSTRATE 1


Mass: 12648.737 Da / Num. of mol.: 1 / Fragment: PTB DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 (DE2) PLYSS / Cell line: BL21 / Gene: PTB DOMAIN OF IRS-1 / Organ: SKELETALSkeleton / Plasmid: PET30B / Gene (production host): PTB DOMAIN OF IRS-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35568
#2: Protein/peptide IL-4 RECEPTOR PHOSPHOPEPTIDE


Mass: 1241.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P24394

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: SET OF IDEAL BOND LENGTHS AND ANGLES USED DURING REFINEMENT: PARALLHDG.PRO IN X-PLOR.
NMR ensembleConformers submitted total number: 1

+
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