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- PDB-2dsq: Structural Basis for the Inhibition of Insulin-like Growth Factor... -

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Basic information

Entry
Database: PDB / ID: 2dsq
TitleStructural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins
Components
  • Insulin-like growth factor IB
  • Insulin-like growth factor-binding protein 1
  • Insulin-like growth factor-binding protein 4
KeywordsPROTEIN BINDING/HORMONE/GROWTH FACTOR / IGF / IGFBP / Insulin / PROTEIN BINDING-HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


regulation of insulin-like growth factor receptor signaling pathway / 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 type B pancreatic cell proliferation / positive regulation of glycoprotein biosynthetic process ...regulation of insulin-like growth factor receptor signaling pathway / 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 type B pancreatic cell proliferation / positive regulation of glycoprotein biosynthetic process / 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 / insulin-like growth factor binding / 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 / ATF4 activates genes in response to endoplasmic reticulum stress / lung vasculature development / exocytic vesicle / cerebellar granule cell precursor proliferation / positive regulation of myoblast proliferation / lung lobe morphogenesis / positive regulation of myelination / tissue regeneration / negative regulation of androgen receptor signaling pathway / cell activation / insulin-like growth factor II binding / glial cell differentiation / positive regulation of calcineurin-NFAT signaling cascade / prostate gland growth / transmembrane receptor protein tyrosine kinase activator activity / insulin-like growth factor I binding / 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 / muscle organ development / positive regulation of cardiac muscle hypertrophy / cellular response to insulin-like growth factor stimulus / 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 / positive regulation of activated T cell proliferation / negative regulation of smooth muscle cell apoptotic process / inner ear development / negative regulation of amyloid-beta formation / myoblast proliferation / regulation of glucose metabolic process / epithelial to mesenchymal transition / negative regulation of tumor necrosis factor production / 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 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / 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 / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of extrinsic apoptotic signaling pathway / insulin receptor binding / Post-translational protein phosphorylation / growth factor activity / cellular response to glucose stimulus / regulation of cell growth / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing
Similarity search - Function
Insulin-like growth factor-binding protein 1 / Insulin-like growth factor-binding protein 4 / Thyroglobulin type-1 / Invariant Chain; Chain I / Omega-AgatoxinV - #20 / Insulin-like growth factor-binding protein family 1-6, chordata / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Omega-AgatoxinV / Insulin-like, subunit E ...Insulin-like growth factor-binding protein 1 / Insulin-like growth factor-binding protein 4 / Thyroglobulin type-1 / Invariant Chain; Chain I / Omega-AgatoxinV - #20 / Insulin-like growth factor-binding protein family 1-6, chordata / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Omega-AgatoxinV / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor I / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Insulin-like growth factor / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Growth factor receptor cysteine-rich domain superfamily / Few Secondary Structures / Irregular / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Insulin-like growth factor 1 / Insulin-like growth factor-binding protein 1 / Insulin-like growth factor-binding protein 4 / Insulin-like growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSitar, T. / Popowicz, G.M. / Siwanowicz, I. / Huber, R. / Holak, T.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis for the inhibition of insulin-like growth factors by insulin-like growth factor-binding proteins.
Authors: Sitar, T. / Popowicz, G.M. / Siwanowicz, I. / Huber, R. / Holak, T.A.
History
DepositionJul 5, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Insulin-like growth factor-binding protein 4
I: Insulin-like growth factor IB
A: Insulin-like growth factor-binding protein 4
C: Insulin-like growth factor IB
G: Insulin-like growth factor-binding protein 1
H: Insulin-like growth factor-binding protein 1


Theoretical massNumber of molelcules
Total (without water)56,7376
Polymers56,7376
Non-polymers00
Water00
1
B: Insulin-like growth factor-binding protein 4
I: Insulin-like growth factor IB
G: Insulin-like growth factor-binding protein 1


Theoretical massNumber of molelcules
Total (without water)28,3693
Polymers28,3693
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area11520 Å2
MethodPISA
2
A: Insulin-like growth factor-binding protein 4
C: Insulin-like growth factor IB
H: Insulin-like growth factor-binding protein 1


Theoretical massNumber of molelcules
Total (without water)28,3693
Polymers28,3693
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-27 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.280, 43.660, 81.150
Angle α, β, γ (deg.)90.00, 91.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Insulin-like growth factor-binding protein 4 / IGFBP-4 / IBP-4 / IGF-binding protein 4


Mass: 9826.498 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P22692
#2: Protein Insulin-like growth factor IB / IGF-IB / Somatomedin C / Mechano growth factor / MGF


Mass: 7663.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P05019, UniProt: Q9NP10*PLUS
#3: Protein Insulin-like growth factor-binding protein 1 / IGFBP-1 / IBP-1 / IGF-binding protein 1 / Placental protein 12 / PP12


Mass: 10878.295 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P08833
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 20% PEG 3350, 0.2M lithium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 22, 2006 / Details: monochromator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 14042 / Num. obs: 13980 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DSP

2dsp


Resolution: 2.8→10 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.792 / SU B: 25.25 / SU ML: 0.506 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.922 / ESU R Free: 0.522 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35708 618 5 %RANDOM
Rwork0.28845 ---
obs0.29188 11658 99.85 %-
all-14042 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.895 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å20 Å2-0.23 Å2
2--6.26 Å20 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 0 0 3072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223164
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9854295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2725397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14823.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.1115486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0521523
X-RAY DIFFRACTIONr_chiral_restr0.0820.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022411
X-RAY DIFFRACTIONr_nbd_refined0.2090.21381
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3850.21
LS refinement shellResolution: 2.8→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 41 -
Rwork0.355 801 -
obs--99.64 %

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