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

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Basic information

Entry
Database: PDB / ID: 2dsp
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 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 / 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 ...regulation of insulin-like growth factor receptor signaling pathway / 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 / negative regulation of vascular associated smooth muscle cell apoptotic process / 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 / IRS-related events triggered by IGF1R / exocytic vesicle / cell activation / positive regulation of calcineurin-NFAT signaling cascade / insulin-like growth factor II binding / type B pancreatic cell proliferation / positive regulation of transcription regulatory region DNA binding / insulin-like growth factor I 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 activated T cell proliferation / positive regulation of cardiac muscle hypertrophy / 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 / regulation of glucose metabolic process / 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 / regulation of cell growth / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of extrinsic apoptotic signaling pathway / Post-translational protein phosphorylation / 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 / negative regulation of canonical Wnt signaling pathway / response to organic cyclic compound / 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 / MAPK cascade / 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 / endoplasmic reticulum lumen / negative regulation of gene expression / signaling receptor binding / 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-binding protein 4 / 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 growth factor I / Insulin-like, subunit E / Insulin-like / Insulin-like growth factor binding protein ...Insulin-like growth factor-binding protein 4 / 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 growth factor I / Insulin-like, subunit E / Insulin-like / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / 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 I / Insulin-like growth factor-binding protein 4 / Insulin-like growth factor I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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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


Theoretical massNumber of molelcules
Total (without water)17,4902
Polymers17,4902
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-11 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.330, 38.990, 61.330
Angle α, β, γ (deg.)90.00, 99.89, 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.: 1 / 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.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 23% PEG 1500, 25mM Tris pH 7, 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: Aug 8, 2004 / 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: 2.5→30 Å / Num. all: 5354 / Num. obs: 5177 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.6 Å / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WQJ

1wqj


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.86 / SU B: 10.243 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.709 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27094 243 4.6 %RANDOM
Rwork0.22046 ---
obs0.22269 5086 99.98 %-
all-5177 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20.63 Å2
2---0.96 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 0 33 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221095
X-RAY DIFFRACTIONr_angle_refined_deg1.372.0071483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6415144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77523.42138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02815167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.219157
X-RAY DIFFRACTIONr_chiral_restr0.090.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02820
X-RAY DIFFRACTIONr_nbd_refined0.2050.2456
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2719
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.23
X-RAY DIFFRACTIONr_mcbond_it0.6291.5757
X-RAY DIFFRACTIONr_mcangle_it1.01921165
X-RAY DIFFRACTIONr_scbond_it1.2653379
X-RAY DIFFRACTIONr_scangle_it2.0754.5318
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 14 -
Rwork0.224 365 -
obs--100 %

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