[English] 日本語
Yorodumi
- PDB-3gf1: SOLUTION STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR 1: A NUCLE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gf1
TitleSOLUTION STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR 1: A NUCLEAR MAGNETIC RESONANCE AND RESTRAINED MOLECULAR DYNAMICS STUDY
ComponentsINSULIN-LIKE GROWTH FACTOR I
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / type II pneumocyte differentiation / neuronal dense core vesicle lumen / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / regulation of establishment or maintenance of cell polarity ...prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / type II pneumocyte differentiation / neuronal dense core vesicle lumen / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / regulation of establishment or maintenance of cell polarity / positive regulation of trophectodermal cell proliferation / positive regulation of glycoprotein biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / proteoglycan biosynthetic process / myotube cell development / positive regulation of transcription regulatory region DNA binding / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of neuroinflammatory response / lung vasculature development / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / bone mineralization involved in bone maturation / positive regulation of cell growth involved in cardiac muscle cell development / IRS-related events triggered by IGF1R / cerebellar granule cell precursor proliferation / negative regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of myoblast proliferation / exocytic vesicle / lung lobe morphogenesis / positive regulation of myelination / negative regulation of androgen receptor signaling pathway / glial cell differentiation / cell activation / prostate gland growth / positive regulation of calcineurin-NFAT signaling cascade / type B pancreatic cell proliferation / transmembrane receptor protein tyrosine kinase activator activity / mammary gland development / exocrine pancreas development / myoblast proliferation / alphav-beta3 integrin-IGF-1-IGF1R complex / regulation of nitric oxide biosynthetic process / myoblast differentiation / cell surface receptor signaling pathway via STAT / positive regulation of Ras protein signal transduction / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of smooth muscle cell migration / growth hormone receptor signaling pathway / positive regulation of DNA binding / negative regulation of interleukin-1 beta production / lung alveolus development / cellular response to insulin-like growth factor stimulus / muscle organ development / branching morphogenesis of an epithelial tube / positive regulation of cardiac muscle hypertrophy / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / type I pneumocyte differentiation / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / inner ear development / positive regulation of activated T cell proliferation / androgen receptor signaling pathway / negative regulation of tumor necrosis factor production / blood vessel remodeling / epithelial to mesenchymal transition / Synthesis, secretion, and deacylation of Ghrelin / activation of protein kinase B activity / positive regulation of glycogen biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of osteoblast differentiation / SHC-related events triggered by IGF1R / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / positive regulation of epithelial cell proliferation / platelet alpha granule lumen / positive regulation of glycolytic process / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of smooth muscle cell proliferation / cellular response to glucose stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / growth factor activity / wound healing / hormone activity / negative regulation of ERK1 and ERK2 cascade / multicellular organism growth / circadian rhythm / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of fibroblast proliferation / cellular response to amyloid-beta / osteoblast differentiation / integrin binding / insulin receptor signaling pathway
Similarity search - Function
Insulin-like, subunit E / Insulin-like / Insulin-like growth factor I / Insulin-like growth factor / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. ...Insulin-like, subunit E / Insulin-like / Insulin-like growth factor I / Insulin-like growth factor / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Insulin-like growth factor 1 / Insulin-like growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsCooke, R.M. / Harvey, T.S. / Campbell, I.D.
CitationJournal: Biochemistry / Year: 1991
Title: Solution structure of human insulin-like growth factor 1: a nuclear magnetic resonance and restrained molecular dynamics study.
Authors: Cooke, R.M. / Harvey, T.S. / Campbell, I.D.
History
DepositionJan 24, 1991Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 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: INSULIN-LIKE GROWTH FACTOR I


Theoretical massNumber of molelcules
Total (without water)7,6641
Polymers7,6641
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 / -
Representative

-
Components

#1: Protein INSULIN-LIKE GROWTH FACTOR I


Mass: 7663.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01343, UniProt: P05019*PLUS
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR ensembleConformers 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