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- PDB-6rva: STRUCTURE OF [ASP58]-IGF-I ANALOGUE -

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Basic information

Entry
Database: PDB / ID: 6rva
TitleSTRUCTURE OF [ASP58]-IGF-I ANALOGUE
ComponentsInsulin-like growth factor I
KeywordsHORMONE / IGF-I ANALOGUE
Function / homology
Function and homology information


glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration ...glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of neuroinflammatory response / bone mineralization involved in bone maturation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / positive regulation of cell growth involved in cardiac muscle cell development / negative regulation of vascular associated smooth muscle cell apoptotic process / IRS-related events triggered by IGF1R / exocytic vesicle / cell activation / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of transcription regulatory region DNA binding / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of Ras protein signal transduction / myoblast differentiation / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / muscle organ development / negative regulation of interleukin-1 beta production / positive regulation of cardiac muscle hypertrophy / positive regulation of activated T cell proliferation / positive regulation of smooth muscle cell migration / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / negative regulation of tumor necrosis factor production / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / positive regulation of DNA binding / SHC-related events triggered by IGF1R / positive regulation of osteoblast differentiation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / positive regulation of epithelial cell proliferation / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / regulation of protein phosphorylation / insulin-like growth factor receptor binding / growth factor activity / wound healing / insulin receptor binding / hormone activity / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / integrin binding / Platelet degranulation / response to heat / regulation of gene expression / cell population proliferation / Ras protein signal transduction / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / protein stabilization / positive regulation of cell migration / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Insulin-like growth factor I / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. ...Insulin-like growth factor I / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Insulin-like growth factor I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJiracek, J. / Zakova, L. / Socha, O.
Funding support United Kingdom, Czech Republic, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K000179/1 United Kingdom
Medical Research Council (United Kingdom)MR/R009066/1 United Kingdom
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Mutations at hypothetical binding site 2 in insulin and insulin-like growth factors 1 and 2 result in receptor- and hormone-specific responses.
Authors: Machackova, K. / Mlcochova, K. / Potalitsyn, P. / Hankova, K. / Socha, O. / Budesinsky, M. / Muzdalo, A. / Lepsik, M. / Cernekova, M. / Radosavljevic, J. / Fabry, M. / Mitrova, K. / ...Authors: Machackova, K. / Mlcochova, K. / Potalitsyn, P. / Hankova, K. / Socha, O. / Budesinsky, M. / Muzdalo, A. / Lepsik, M. / Cernekova, M. / Radosavljevic, J. / Fabry, M. / Mitrova, K. / Chrudinova, M. / Lin, J. / Yurenko, Y. / Hobza, P. / Selicharova, I. / Zakova, L. / Jiracek, J.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Insulin-like growth factor I


Theoretical massNumber of molelcules
Total (without water)7,7071
Polymers7,7071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6050 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Insulin-like growth factor I / IGF-I / Mechano growth factor / MGF / Somatomedin-C


Mass: 7706.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1, IBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05019

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
132isotropic12D 1H-15N HSQC
143isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.18 mM [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 95% H2O/5% D2Onon-labeled95% H2O/5% D2O
solution20.05 mM [U-13C; U-15N] [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 95% H2O/5% D2O15N_13C_labeled95% H2O/5% D2O
solution30.05 mM [U-13C; U-15N] [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 100% D2O15N_13C_labeled_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.18 mM[L-Asp58]-IGF-1 analoguenatural abundance1
0.01 %sodium azidenatural abundance1
50 mMacetic acid[U-2H]1
0.05 mM[L-Asp58]-IGF-1 analogue[U-13C; U-15N]2
0.01 %sodium azidenatural abundance2
50 mMacetic acid[U-2H]2
0.05 mM[L-Asp58]-IGF-1 analogue[U-13C; U-15N]3
0.01 %sodium azidenatural abundance3
50 mMacetic acid[U-2H]3
Sample conditionsIonic strength: 0 Not defined / Label: conditions_40C / pH: 3.0 / Pressure: 1 atm / Temperature: 313.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.44Schwieters, Kuszewski, Tjandra and Clorerefinement
Xplor-NIH2.44Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr Analysis2.4.2Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides and Ernest D. Lauechemical shift assignment
CcpNmr Analysis2.4.2Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides and Ernest D. Lauepeak picking
TopSpinBruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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