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- PDB-1bqt: THREE-DIMENSIONAL STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR-I... -

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Entry
Database: PDB / ID: 1bqt
TitleTHREE-DIMENSIONAL STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR-I (IGF-I) DETERMINED BY 1H-NMR AND DISTANCE GEOMETRY, 6 STRUCTURES
ComponentsINSULIN-LIKE GROWTH FACTOR-I
KeywordsGROWTH FACTOR / INSULIN
Function / homology
Function and homology information


glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of trophectodermal cell proliferation / prostate gland stromal morphogenesis / positive regulation of glycoprotein biosynthetic process / positive regulation of type B pancreatic cell proliferation / type II pneumocyte differentiation ...glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of trophectodermal cell proliferation / prostate gland stromal morphogenesis / positive regulation of glycoprotein biosynthetic process / positive regulation of type B pancreatic cell proliferation / type II pneumocyte differentiation / neuronal dense core vesicle lumen / proteoglycan biosynthetic process / regulation of establishment or maintenance of cell polarity / chondroitin sulfate proteoglycan biosynthetic process / myotube cell development / positive regulation of transcription regulatory region DNA binding / negative regulation of neuroinflammatory response / 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 / negative regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of cerebellar granule cell precursor proliferation / exocytic vesicle / lung vasculature development / cerebellar granule cell precursor proliferation / positive regulation of myoblast proliferation / lung lobe morphogenesis / positive regulation of myelination / negative regulation of androgen receptor signaling pathway / cell activation / glial cell differentiation / positive regulation of calcineurin-NFAT signaling cascade / prostate gland growth / transmembrane receptor protein tyrosine kinase activator activity / type B pancreatic cell proliferation / mammary gland development / exocrine pancreas development / alphav-beta3 integrin-IGF-1-IGF1R complex / myoblast differentiation / cell surface receptor signaling pathway via STAT / regulation of nitric oxide biosynthetic process / 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 / positive regulation of cardiac muscle hypertrophy / branching morphogenesis of an epithelial tube / androgen receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / negative regulation of release of cytochrome c from mitochondria / type I pneumocyte differentiation / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / positive regulation of activated T cell proliferation / inner ear development / myoblast proliferation / negative regulation of tumor necrosis factor production / epithelial to mesenchymal transition / blood vessel remodeling / Synthesis, secretion, and deacylation of Ghrelin / activation of protein kinase B activity / positive regulation of glycogen biosynthetic process / positive regulation of osteoblast differentiation / SHC-related events triggered by IGF1R / postsynaptic modulation of chemical synaptic transmission / 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 smooth muscle cell proliferation / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / positive regulation of glycolytic process / positive regulation of epithelial cell proliferation / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / growth factor activity / cellular response to glucose stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / circadian rhythm / hormone activity / negative regulation of ERK1 and ERK2 cascade / multicellular organism growth / integrin binding / 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsSato, A. / Nishimura, S. / Ohkubo, T. / Kyogoku, Y. / Koyama, S. / Kobayashi, M. / Yasuda, T. / Kobayashi, Y.
Citation
Journal: Int.J.Pept.Protein Res. / Year: 1993
Title: Three-dimensional structure of human insulin-like growth factor-I (IGF-I) determined by 1H-NMR and distance geometry.
Authors: Sato, A. / Nishimura, S. / Ohkubo, T. / Kyogoku, Y. / Koyama, S. / Kobayashi, M. / Yasuda, T. / Kobayashi, Y.
#1: Journal: J.Biochem.(Tokyo) / Year: 1992
Title: 1H-NMR Assignment and Secondary Structure of Human Insulin-Like Growth Factor-I (Igf-I) in Solution
Authors: Sato, A. / Nishimura, S. / Ohkubo, T. / Kyogoku, Y. / Koyama, S. / Kobayashi, M. / Yasuda, T. / Kobayashi, Y.
History
DepositionAug 18, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)6 / 100target function
Representative

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Components

#1: Protein INSULIN-LIKE GROWTH FACTOR-I / SOMATOMEDIN C


Mass: 7663.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05019
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121HOHAHA
131NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR SPECTROSCOPY

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Sample preparation

DetailsContents: H2O/D2O=9/1 CONTAINING 10 ACETIC ACID-D4
Sample conditionspH: 3 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
JEOL GSX500JEOLGSX5005001
Bruker AMX500BrukerAMX5005002

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Processing

NMR software
NameClassification
DADASstructure solution
DADASrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 6

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