[English] 日本語
Yorodumi
- PDB-1gk5: Solution Structure the mEGF/TGFalpha44-50 chimeric growth factor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gk5
TitleSolution Structure the mEGF/TGFalpha44-50 chimeric growth factor
ComponentsPro-epidermal growth factor,Protransforming growth factor alpha
KeywordsGROWTH FACTOR / EGF GROWTH FACTOR / CHIMERIC
Function / homology
Function and homology information


Signaling by ERBB4 / EGFR interacts with phospholipase C-gamma / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / PI3K events in ERBB2 signaling / SHC1 events in ERBB2 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by ERBB2 / GAB1 signalosome ...Signaling by ERBB4 / EGFR interacts with phospholipase C-gamma / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / PI3K events in ERBB2 signaling / SHC1 events in ERBB2 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by ERBB2 / GAB1 signalosome / ERBB2 Regulates Cell Motility / NOTCH3 Activation and Transmission of Signal to the Nucleus / Downregulation of ERBB2 signaling / EGFR downregulation / positive regulation of hyaluronan biosynthetic process / negative regulation of secretion / negative regulation of cholesterol efflux / hepatocyte proliferation / Extra-nuclear estrogen signaling / regulation of protein transport / RAF/MAP kinase cascade / PIP3 activates AKT signaling / positive regulation of epithelial tube formation / positive regulation of cerebellar granule cell precursor proliferation / Cargo recognition for clathrin-mediated endocytosis / regulation of protein localization to cell surface / positive regulation of protein localization to early endosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Platelet degranulation / cerebellar granule cell precursor proliferation / Clathrin-mediated endocytosis / regulation of calcium ion import / transmembrane receptor protein tyrosine kinase activator activity / Cargo concentration in the ER / positive regulation of ubiquitin-dependent protein catabolic process / COPII-mediated vesicle transport / epidermal growth factor receptor binding / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / regulation of receptor signaling pathway via JAK-STAT / positive regulation of DNA binding / ERBB2-EGFR signaling pathway / branching morphogenesis of an epithelial tube / Signaling by EGFR / positive regulation of cell division / positive regulation of receptor internalization / positive regulation of phosphorylation / mammary gland alveolus development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / GAB1 signalosome / ERK1 and ERK2 cascade / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of endothelial cell migration / positive regulation of mitotic nuclear division / guanyl-nucleotide exchange factor activity / epithelial cell proliferation / positive regulation of epithelial cell proliferation / growth factor activity / EGFR downregulation / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / epidermal growth factor receptor signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cytoplasmic vesicle / angiogenesis / basolateral plasma membrane / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / intracellular signal transduction / receptor ligand activity / positive regulation of cell population proliferation / calcium ion binding / positive regulation of gene expression / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Pro-epidermal growth factor / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / Six-bladed beta-propeller, TolB-like / Laminin ...Pro-epidermal growth factor / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / Six-bladed beta-propeller, TolB-like / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Pro-epidermal growth factor / Protransforming growth factor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING
AuthorsChamberlin, S.G. / Brennan, L. / Puddicombe, S.M. / Davies, D.E. / Turner, D.L.
Citation
Journal: Eur.J.Biochem. / Year: 2001
Title: Solution Structure of the Megf/Tgfalpha44-50 Chimeric Growth Factor.
Authors: Chamberlin, S. / Brennan, L. / Puddicombe, S. / Davies, D. / Turner, D.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: The Interaction of an Epidermal Growth Factor/ Transforming Growth Factor Alpha Tail Chimera with the Human Epidermal Growth Factor Receptor Reveals Unexpected Complexities
Authors: Puddicombe, S.M. / Wood, L. / Chamberlin, S.G. / Davies, D.E.
History
DepositionAug 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_fragment / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pro-epidermal growth factor,Protransforming growth factor alpha


Theoretical massNumber of molelcules
Total (without water)5,2581
Polymers5,2581
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)10 / 50LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein/peptide Pro-epidermal growth factor,Protransforming growth factor alpha / EGF


Mass: 5257.785 Da / Num. of mol.: 1 / Fragment: UNP residues 977-1018,UNP residues 83-89
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES 977-1018 AND HUMAN TRANSFORMING GROWTH FACTOR ALPHA RESIDUES 83-89,THE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES ...Details: THE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES 977-1018 AND HUMAN TRANSFORMING GROWTH FACTOR ALPHA RESIDUES 83-89,THE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES 977-1018 AND HUMAN TRANSFORMING GROWTH FACTOR ALPHA RESIDUES 83-89
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Egf, TGFA / Production host: Komagataella pastoris (fungus) / References: UniProt: P01132, UniProt: P01135
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D-1H-NOESY 2D-1H-TOCSY 2D-1H-COSY

-
Sample preparation

Sample conditionspH: 3 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian VXR500 / Manufacturer: Varian / Model: VXR500 / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
INDYANABRENNAN L, TURNER DL, MESSIAS AM, TEODORO ML, LEGALL J, SANTOS H, XAVIER AX.refinement
INDYANAstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / 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