[English] 日本語
Yorodumi
- PDB-4tgf: SOLUTION STRUCTURES OF HUMAN TRANSFORMING GROWTH FACTOR ALPHA DER... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tgf
TitleSOLUTION STRUCTURES OF HUMAN TRANSFORMING GROWTH FACTOR ALPHA DERIVED FROM 1*H NMR DATA
ComponentsDES-VAL-1,VAL-2,TRANSFORMING GROWTH FACTOR, ALPHA
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


hepatocyte proliferation / Cargo concentration in the ER / Inhibition of Signaling by Overexpressed EGFR / COPII-mediated vesicle transport / EGFR interacts with phospholipase C-gamma / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of cell division ...hepatocyte proliferation / Cargo concentration in the ER / Inhibition of Signaling by Overexpressed EGFR / COPII-mediated vesicle transport / EGFR interacts with phospholipase C-gamma / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of cell division / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mammary gland alveolus development / GAB1 signalosome / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / positive regulation of epithelial cell proliferation / EGFR downregulation / clathrin-coated endocytic vesicle membrane / growth factor activity / epidermal growth factor receptor signaling pathway / ER to Golgi transport vesicle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / receptor ligand activity / intracellular signal transduction / positive regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Laminin / Laminin / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Protransforming growth factor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsKline, T.P. / Brown, F.K. / Brown, S.C. / Jeffs, P.W. / Kopple, K.D. / Mueller, L.
Citation
Journal: Biochemistry / Year: 1990
Title: Solution structures of human transforming growth factor alpha derived from 1H NMR data.
Authors: Kline, T.P. / Brown, F.K. / Brown, S.C. / Jeffs, P.W. / Kopple, K.D. / Mueller, L.
#1: Journal: Biochemistry / Year: 1989
Title: 1H NMR Assignment and Secondary Structural Elements of Human Transforming Growth Factor Alpha
Authors: Brown, S.C. / Mueller, L. / Jeffs, P.W.
History
DepositionJun 13, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DES-VAL-1,VAL-2,TRANSFORMING GROWTH FACTOR, ALPHA


Theoretical massNumber of molelcules
Total (without water)5,5601
Polymers5,5601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / -
Representative

-
Components

#1: Protein/peptide DES-VAL-1,VAL-2,TRANSFORMING GROWTH FACTOR, ALPHA


Mass: 5560.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01135

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Processing

NMR software
NameDeveloperClassification
DSPACEHARE RESEARCH, INC.refinement
X-PLORBRUNGERrefinement
NMR ensembleConformers submitted total number: 4

+
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