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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 / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / myotube cell development / proteoglycan biosynthetic process / neuronal dense core vesicle lumen ...glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / myotube cell development / proteoglycan biosynthetic process / neuronal dense core vesicle lumen / positive regulation of transcription regulatory region DNA binding / positive regulation of cell growth involved in cardiac muscle cell development / negative regulation of neuroinflammatory response / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / bone mineralization involved in bone maturation / negative regulation of vascular associated smooth muscle cell apoptotic process / exocytic vesicle / positive regulation of glycoprotein biosynthetic process / myoblast differentiation / positive regulation of calcineurin-NFAT signaling cascade / cell activation / positive regulation of myelination / positive regulation of insulin-like growth factor receptor signaling pathway / alphav-beta3 integrin-IGF-1-IGF1R complex / cell surface receptor signaling pathway via STAT / activation of protein kinase B activity / positive regulation of activated T cell proliferation / positive regulation of smooth muscle cell migration / positive regulation of DNA binding / growth hormone receptor signaling pathway / negative regulation of interleukin-1 beta production / muscle organ development / negative regulation of release of cytochrome c from mitochondria / positive regulation of cardiac muscle hypertrophy / negative regulation of amyloid-beta formation / positive regulation of osteoblast differentiation / myoblast proliferation / negative regulation of smooth muscle cell apoptotic process / epithelial to mesenchymal transition / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of tumor necrosis factor production / skeletal system development / positive regulation of glycogen biosynthetic process / protein kinase activator activity / postsynaptic modulation of chemical synaptic transmission / positive regulation of vascular associated smooth muscle cell proliferation / SHC-related events triggered by IGF1R / positive regulation of Ras protein signal transduction / insulin-like growth factor receptor signaling pathway / insulin-like growth factor receptor binding / positive regulation of D-glucose import across plasma membrane / positive regulation of mitotic nuclear division / positive regulation of epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of glycolytic process / platelet alpha granule lumen / positive regulation of fibroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion / wound healing / insulin receptor binding / growth factor activity / circadian rhythm / hormone activity / integrin binding / cell population proliferation / insulin receptor signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / osteoblast differentiation / cellular response to amyloid-beta / regulation of gene expression / Platelet degranulation / response to heat / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / postsynapse / protein stabilization / positive regulation of cell migration / negative regulation of gene expression / positive regulation of gene expression / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / glutamatergic synapse / signal transduction / positive regulation of transcription by RNA polymerase II / : / extracellular region
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 / 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
Revision 1.4Nov 6, 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

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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
Has protein modificationY

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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 / 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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