[English] 日本語
Yorodumi
- PDB-1ks6: Transforming Growth Factor Beta type II receptor ligand binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ks6
TitleTransforming Growth Factor Beta type II receptor ligand binding domain
ComponentsTRANSFORMING GROWTH FACTOR BETA TYPE II RECEPTOR
KeywordsHORMONE/GROWTH FACTOR / THREE FINGER TOXIN FOLD / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


TGF-beta receptor signaling activates SMADs / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor activity, type II / detection of hypoxia / activin receptor activity / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / transforming growth factor beta receptor activity ...TGF-beta receptor signaling activates SMADs / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor activity, type II / detection of hypoxia / activin receptor activity / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / transforming growth factor beta receptor activity / response to xenobiotic stimulus => GO:0009410 / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / eye development / cell activation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / activin binding / type I transforming growth factor beta receptor binding / cell-cell junction organization / glycosaminoglycan binding / response to cholesterol / transforming growth factor beta binding / regulation of growth / face morphogenesis / SMAD binding / embryonic organ development / positive regulation of epithelial to mesenchymal transition / positive regulation of stress fiber assembly / transforming growth factor beta receptor signaling pathway / extracellular matrix / caveola / response to progesterone / positive regulation of protein secretion / lung development / cellular response to growth factor stimulus / positive regulation of reactive oxygen species metabolic process / cell migration / heart development / membrane => GO:0016020 / receptor complex / response to hypoxia / positive regulation of cell migration / membrane raft / external side of plasma membrane / protein phosphorylation / protein serine/threonine kinase activity / apoptotic process / positive regulation of gene expression / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site ...Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
TGF-beta receptor type-2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMarlow, M.S. / Brown, C.B. / Barnett, J.V. / Krezel, A.M.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Solution structure of the chick TGFb type II receptor ligand binding domain
Authors: Marlow, M.S. / Brown, C.B. / Barnett, J.V. / Krezel, A.M.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSFORMING GROWTH FACTOR BETA TYPE II RECEPTOR


Theoretical massNumber of molelcules
Total (without water)12,0671
Polymers12,0671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #6closest to the average

-
Components

#1: Protein TRANSFORMING GROWTH FACTOR BETA TYPE II RECEPTOR / TGFb type II receptor


Mass: 12066.688 Da / Num. of mol.: 1
Fragment: LIGAND BINDING DOMAIN, SEQUENCE DATABASE RESIDUES 34-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET-32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q90999

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY
142HNCA-J

-
Sample preparation

Details
Solution-IDContentsSolvent system
11-2mM TbRII Natural Abundance100% D2O
21-2mM TbRII U-15N,13C90% H2O/10% D2O
31-2mM TbRII U-15N,13C100% D2O
Sample conditionsIonic strength: 1 / pH: 6.5 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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://pdbjlvh1.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