[English] 日本語
Yorodumi
- PDB-2bbu: solution structure of mouse socs3 in complex with a phosphopeptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bbu
Titlesolution structure of mouse socs3 in complex with a phosphopeptide from the gp130 receptor
Components
  • GP130 PHOSPHOPEPTIDE
  • Suppressor of cytokine signaling 3
KeywordsCYTOKINE REGULATOR / SH2 DOMAIN / EXTENDED SH2 SUBDOMAIN / PEST MOTIF / PROTEIN COMPLEX / PHOSPHOPEPTIDE
Function / homology
Function and homology information


Regulation of IFNG signaling / PTK6 Activates STAT3 / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / oncostatin-M receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interferon gamma signaling / Interleukin-27 signaling / triglyceride mobilization ...Regulation of IFNG signaling / PTK6 Activates STAT3 / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / oncostatin-M receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interferon gamma signaling / Interleukin-27 signaling / triglyceride mobilization / Interleukin-6 signaling / Interleukin-35 Signalling / oncostatin-M receptor complex / Interferon alpha/beta signaling / oncostatin-M-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / interleukin-6 receptor activity / interleukin-6 binding / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / negative regulation of tyrosine phosphorylation of STAT protein / regulation of Notch signaling pathway / interleukin-6 receptor binding / interleukin-11-mediated signaling pathway / cellular response to interleukin-17 / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / Neddylation / positive regulation of astrocyte differentiation / Antigen processing: Ubiquitination & Proteasome degradation / intestinal epithelial cell development / protein tyrosine kinase inhibitor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex / miRNA binding / cytokine receptor activity / neuronal cell body membrane / glycogen metabolic process / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of cytosolic calcium ion concentration / protein tyrosine kinase activator activity / cytokine binding / positive regulation of smooth muscle cell migration / growth factor binding / phosphatidylinositol phosphate biosynthetic process / cell surface receptor signaling pathway via JAK-STAT / positive regulation of osteoblast differentiation / coreceptor activity / negative regulation of signal transduction / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of insulin receptor signaling pathway / phosphotyrosine residue binding / cellular response to leukemia inhibitory factor / response to cytokine / positive regulation of cell differentiation / regulation of protein phosphorylation / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / negative regulation of inflammatory response / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / cell differentiation / receptor complex / protein ubiquitination / intracellular signal transduction / membrane raft / external side of plasma membrane / neuronal cell body / dendrite / positive regulation of cell population proliferation / signal transduction / extracellular space / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Suppressor of cytokine signalling 3 / SOCS3, SH2 domain / suppressors of cytokine signalling / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding ...Suppressor of cytokine signalling 3 / SOCS3, SH2 domain / suppressors of cytokine signalling / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / SH2 domain / SHC Adaptor Protein / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Suppressor of cytokine signaling 3 / Interleukin-6 receptor subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing distance geometry torsion angle dynamics
AuthorsBabon, J.J. / Yao, S. / Norton, R.S.
CitationJournal: Mol.Cell / Year: 2006
Title: The Structure of SOCS3 Reveals the Basis of the Extended SH2 Domain Function and Identifies an Unstructured Insertion That Regulates Stability
Authors: Babon, J.J. / McManus, E.J. / Yao, S. / DeSouza, D.P. / Mielke, L.A. / Sprigg, N.S. / Willson, T.A. / Hilton, D.J. / Nicola, N.A. / Baca, M. / Nicholson, S.E. / Norton, R.S.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Suppressor of cytokine signaling 3
B: GP130 PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)19,5672
Polymers19,5672
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)20 / 200structures with favorable non-bond energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Suppressor of cytokine signaling 3 / SOCS-3 / Cytokine-inducible SH2 protein 3 / CIS-3 / Protein EF-10


Mass: 17961.236 Da / Num. of mol.: 1 / Fragment: KIR/ESS/SH2 DOMAIN/PEST MOTIF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SOCS3 / Plasmid: JLIC1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O35718
#2: Protein/peptide GP130 PHOSPHOPEPTIDE


Mass: 1605.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC PHOSPHOPEPTIDE / References: UniProt: Q00560*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY
1452D NOESY
1552D TOCSY
1642D NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.3mM U-15N-13C-SOCS3/0.3mM phophopeptide, 20mM Na-phosphate, pH 6.7, 2mM DTT, 1mM edta, 50mM glutamate, 50mM Arginine, 5% D2O95% H20, 5% D2O
20.3mM U-15N-SOCS3/0.3mM phophopeptide, 20mM Na-phosphate, pH 6.7, 2mM DTT, 1mM edta, 50mM glutamate, 50mM Arginine, 5% D2O95% H20, 5% D2O
30.3mM U-13C-SOCS3/0.3mM phophopeptide, 20mM Na-phosphate, pH 6.7, 2mM DTT, 1mM edta, 50mM glutamate, 50mM Arginine, 5% D2O95% H20, 5% D2O
40.3mM SOCS3/0.3mM phophopeptide, 20mM Na-phosphate, pH 6.7, 2mM DTT, 1mM edta, 50mM glutamate, 50mM Arginine, 5% D2O95% H20, 5% D2O
50.3mM SOCS3/0.3mM phophopeptide, 20mM Na-phosphate, pH 6.7, 2mM DTT, 1mM edta, 50mM glutamate, 50mM Arginine, 5% D2O100% D2O
Sample conditionsIonic strength: 50mM / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDeLagliodata analysis
XwinNMRcollection
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: simulated annealing distance geometry torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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