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- PDB-1pmx: INSULIN-LIKE GROWTH FACTOR-I BOUND TO A PHAGE-DERIVED PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1pmx
TitleINSULIN-LIKE GROWTH FACTOR-I BOUND TO A PHAGE-DERIVED PEPTIDE
Components
  • IGF-1 ANTAGONIST F1-1
  • Insulin-like growth factor IB
KeywordsHORMONE/GROWTH FACTOR / IGF-I / PEPTIDE BINDING / HIGH AFFINITY LIGAND / HORMONE-GROWTH FACTOR COMPLEX
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 / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsSkelton, N.J.
Citation
Journal: Biochemistry / Year: 2003
Title: Complex with a Phage Display-Derived Peptide Provides Insight into the Function of Insulin-like Growth Factor I
Authors: Schaffer, M.L. / Deshayes, K. / Nakamura, G. / Sidhu, S. / Skelton, N.J.
#1: Journal: Chem.Biol. / Year: 2002
Title: Rapid Identification of Small Binding Motifs with High-Throughput Phage Display. Discovery of Peptidic Antagonists of Igf-1 Function
Authors: Deshayes, K. / Schaffer, M.L. / Skelton, N.J. / Nakamura, G.R. / Kadkhodayan, S. / Sidhu, S.S.
History
DepositionJun 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 20, 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 IB
B: IGF-1 ANTAGONIST F1-1


Theoretical massNumber of molelcules
Total (without water)9,5432
Polymers9,5432
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)20 / 100LEAST VIOLATION OF EXPERIMENTAL RESTRAINTS
RepresentativeModel #1closest to the average, fewest violations

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Components

#1: Protein Insulin-like growth factor IB / IGF-IB / Somatomedin C


Mass: 7663.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBKIGF2B / Production host: Escherichia coli (E. coli) / Strain (production host): 43E7 / References: UniProt: P05019
#2: Protein/peptide IGF-1 ANTAGONIST F1-1


Mass: 1879.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SEQUENCE DERIVED FROM PHAGE DISPLAY LIBRARY AND PREPARED BY CHEMICAL SYNTHESIS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
121HNHA
131D-HNHB
1413D 15N-SEPARATED LOW MIXING TIME TOCSY
1512D-15N-FILTERED NOESY
1613D 13C-SEPARATED NOESY
1713D-13 FILTERED
18113C-EDITED NOESY
1912D-13C-FILTERED NOESY
NMR detailsText: THE RESONANCE ASSIGNMENTS WERE DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 MM IGF-I (15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATE
21.4 MM IGF-I (13C,15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATE
31.4 MM IGF-I (13C,15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATED2O
Sample conditionsIonic strength: 25 mM / pH: 5.1 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS2000.1ACCELRYSrefinement
XwinNMR3.1ACCELRYSstructure solution
Felix98ACCELRYSstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: THE COMPLEX WAS DETERMINED USING A TOTAL OF 905 NOE DISTANCE RESTRAINTS (146 INTRA RESIDUE, 203 SEQUENTIAL, 232 MEDIUM RANGE, 237 LONG-RANGE AND 87 INTERMOLECULAR), 24 HYDROGEN BOND ...Details: THE COMPLEX WAS DETERMINED USING A TOTAL OF 905 NOE DISTANCE RESTRAINTS (146 INTRA RESIDUE, 203 SEQUENTIAL, 232 MEDIUM RANGE, 237 LONG-RANGE AND 87 INTERMOLECULAR), 24 HYDROGEN BOND RESTRAINTS, 139 DIHEDRAL ANGLE RESTRAINTS (72 PHI, 44 PSI AND 23 CHI-1). THE BEST 20 CONFORMERS (OF 100) HAD NO DISTANCE VIOLATIONS GREATER THAN 0.11A AND NO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 1.5 DEGREES. RMSD FROM EXPERIMENTAL DISTANCE RESTRAINTS WAS 0.0049+/-0.0008. THE MEAN BACKBONE RMSD FROM THE MEAN STRUCTURE WAS 0.35 +/- 0.06 A FOR N, CA AND C ATOMS OF RESIDUES 3-26, 42-63 of IGF-I AND RESIDUES 3-15 OF THE PEPTIDE. 82% (17%) OF RESIDUES WERE IN THE MOST FAVOURED (ALLOWED) REGION OF PHI/PSI SPACE; NO RESIDUES WERE CONSISTENTLY IN THE DISALLOWED REGION.
NMR representativeSelection criteria: closest to the average, fewest violations
NMR ensembleConformer selection criteria: LEAST VIOLATION OF EXPERIMENTAL RESTRAINTS
Conformers calculated total number: 100 / Conformers submitted total number: 20

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