[English] 日本語
Yorodumi
- PDB-1plo: TRANSFORMING GROWTH FACTOR-BETA TYPE II RECEPTOR EXTRACELLULAR DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1plo
TitleTRANSFORMING GROWTH FACTOR-BETA TYPE II RECEPTOR EXTRACELLULAR DOMAIN
ComponentsTGF-beta receptor type II
KeywordsCytokine receptor / Three-Finger Toxin Fold
Function / homology
Function and homology information


positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / activin receptor activity / TGFBR2 MSI Frameshift Mutants in Cancer ...positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / activin receptor activity / TGFBR2 MSI Frameshift Mutants in Cancer / miRNA transport / transforming growth factor beta ligand-receptor complex / type III transforming growth factor beta receptor binding / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / cardiac left ventricle morphogenesis / secondary palate development / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / endocardial cushion fusion / positive regulation of T cell tolerance induction / membranous septum morphogenesis / lung lobe morphogenesis / TGFBR3 regulates TGF-beta signaling / positive regulation of NK T cell differentiation / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transforming growth factor beta receptor activity, type II / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type III / regulation of stem cell proliferation / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / activin binding / type I transforming growth factor beta receptor binding / SMAD protein signal transduction / pattern specification process / positive regulation of CD4-positive, alpha-beta T cell proliferation / outflow tract septum morphogenesis / glycosaminoglycan binding / regulation of stem cell differentiation / response to cholesterol / kinase activator activity / embryonic cranial skeleton morphogenesis / transforming growth factor beta binding / aortic valve morphogenesis / lens development in camera-type eye / embryonic hemopoiesis / atrioventricular valve morphogenesis / positive regulation of mesenchymal cell proliferation / artery morphogenesis / trachea formation / smoothened signaling pathway / ventricular septum morphogenesis / branching involved in blood vessel morphogenesis / roof of mouth development / blood vessel development / SMAD binding / heart looping / TGF-beta receptor signaling activates SMADs / outflow tract morphogenesis / positive regulation of epithelial cell migration / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / vasculogenesis / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / gastrulation / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cellular response to growth factor stimulus / brain development / caveola / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / UCH proteinases / heart development / regulation of cell population proliferation / regulation of gene expression / molecular adaptor activity / in utero embryonic development / receptor complex / membrane raft / response to xenobiotic stimulus / external side of plasma membrane / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / extracellular space / extracellular region / ATP binding / membrane / metal ion binding
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 / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase ...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 / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / substructure distance geometry, full structure distance geometry-simulated annealing; torsion angle dynamics
AuthorsDeep, S. / Walker III, K.P. / Shu, Z. / Hinck, A.P.
CitationJournal: Biochemistry / Year: 2003
Title: Solution structure and backbone dynamics of the TGF-beta type II receptor extracellular domain
Authors: Deep, S. / Walker III, K.P. / Shu, Z. / Hinck, A.P.
History
DepositionJun 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TGF-beta receptor type II


Theoretical massNumber of molelcules
Total (without water)13,8111
Polymers13,8111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1fewest violations, lowest energy

-
Components

#1: Protein TGF-beta receptor type II / TGFR-2 / TGF-beta type II receptor


Mass: 13810.606 Da / Num. of mol.: 1 / Mutation: N19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37173, EC: 2.7.1.37
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2233D 13C-separated NOESY
2334D 13C-separated NOESY
1423D 15N edited, 13C-edited 1H-1H NOESY
1513D 15N-edited,15N-edited 1H-1H NOESY
3641H-15H 1-bond residual dipolar coupling (2D IPAP-HSQC)
37513C-13CO residual dipolar coupling (3D (HA)CA(CO)NH
38513Calpha-13CO residual dipolar coupling (3D Ca-coupled HNCO)
NMR detailsText: This structure was determined by refining simultaneously against NOE, J-coupling, dihedral angle, and residual dipolar coupling constraints

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM ecTbR2 U-15N, 25mM sodium acetate, 25mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
21mM ecTbR2 U-15N, 13C, 25mM sodium acetate, 25mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
31mM ecTbR2 U-15N, 13C, 25mM sodium acetate, 25mM NaCl, 99.99% D2O99.99% D2O
41mM ecTbR2 U-15N, 25mM sodium acetate, 25mM NaCl, 4% (w/v) 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (6-O-PC) and 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (14-O-PC) mixed in a molar ratio of 1:3, 95% H2O, 5% D2O95% H2O/5% D2O
51mM ecTbR2 U-15N, 13C, 25mM sodium acetate, 25mM NaCl, 4% (w/v) 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (6-O-PC) and 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (14-O-PC) mixed in a molar ratio of 1:3, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125mM sodium acetate, 25mM NaCl, pH 5.5 5.5ambient 300 K
225mM sodium acetate, 25mM NaCl 5.1ambient 300 K
325mM sodium acetate, 25mM NaCl 5.5ambient 313 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 DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE5002

-
Processing

NMR softwareName: XPLOR_NIH / Version: 1.06
Developer: Clore, G.M., Kuszewski, J., Schwieters, C.D., Tjandra, N.
Classification: refinement
RefinementMethod: substructure distance geometry, full structure distance geometry-simulated annealing; torsion angle dynamics
Software ordinal: 1
Details: structures are based on a total of 1583 constraints, 1168 are NOE distance, 138 are dihedredral angle, 58 are 3JHNHa coupling constant, 219 are residual dipolar couplings,
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
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