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- PDB-1wqj: Structural Basis for the Regulation of Insulin-Like Growth Factor... -

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Basic information

Entry
Database: PDB / ID: 1wqj
TitleStructural Basis for the Regulation of Insulin-Like Growth Factors (IGFs) by IGF Binding Proteins (IGFBPs)
Components
  • Insulin-like growth factor IB
  • Insulin-like growth factor binding protein 4
KeywordsPROTEIN BINDING/HORMONE/GROWTH FACTOR / PROTEIN-PROTEIN COMPLEX / DISULFIDE RICH / DISULFIDE BOND LADDER / 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 / positive regulation of glycoprotein biosynthetic process / proteoglycan 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 / positive regulation of glycoprotein biosynthetic process / proteoglycan biosynthetic process / myotube cell development / negative regulation of neuroinflammatory response / positive regulation of transcription regulatory region DNA 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 / exocytic vesicle / insulin-like growth factor II binding / cell activation / type B pancreatic cell proliferation / positive regulation of calcineurin-NFAT signaling cascade / transmembrane receptor protein tyrosine kinase activator activity / insulin-like growth factor I binding / alphav-beta3 integrin-IGF-1-IGF1R complex / cell surface receptor signaling pathway via STAT / myoblast differentiation / positive regulation of Ras protein signal transduction / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / growth hormone receptor signaling pathway / negative regulation of interleukin-1 beta production / positive regulation of DNA binding / muscle organ development / positive regulation of smooth muscle cell migration / positive regulation of cardiac muscle hypertrophy / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / positive regulation of activated T cell proliferation / negative regulation of smooth muscle cell apoptotic process / regulation of glucose metabolic process / negative regulation of tumor necrosis factor production / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / SHC-related events triggered by IGF1R / positive regulation of osteoblast differentiation / activation of protein kinase B activity / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / 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 / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / regulation of cell growth / insulin receptor binding / growth factor activity / wound healing / negative regulation of canonical Wnt signaling pathway / : / hormone activity / positive regulation of fibroblast proliferation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / integrin binding / MAPK cascade / insulin receptor signaling pathway / Platelet degranulation / response to heat / regulation of gene expression / Ras protein signal transduction / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / protein stabilization / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / 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-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, subunit E / Insulin-like / Insulin-like growth factor I / 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, 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSiwanowicz, I. / Popowicz, G.M. / Wisniewska, M. / Huber, R. / Kuenkele, K.P. / Lang, K. / Engh, R.A. / Holak, T.A.
CitationJournal: Structure / Year: 2005
Title: Structural basis for the regulation of insulin-like growth factors by IGF binding proteins
Authors: Siwanowicz, I. / Popowicz, G.M. / Wisniewska, M. / Huber, R. / Kuenkele, K.P. / Lang, K. / Engh, R.A. / Holak, T.A.
History
DepositionSep 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 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


Theoretical massNumber of molelcules
Total (without water)16,1622
Polymers16,1622
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.470, 54.280, 74.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details1:1 (B:I) stechiometry binary complex, single complex molecule per assymetric unit

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Components

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


Mass: 8498.120 Da / Num. of mol.: 1 / Fragment: NBP-4 (residues 3-82)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET 28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22692
#2: Protein Insulin-like growth factor IB / IGF-I / 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) / References: UniProt: P05019
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 23% PEG 1500, 25mM Tris, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.6→37 Å / Num. all: 86002 / Num. obs: 17605 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.044 / Rsym value: 0.04 / Net I/σ(I): 16.86
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 5.45 / Num. unique all: 1964 / Rsym value: 0.144 / % possible all: 76.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H59

1h59


Resolution: 1.6→31.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.92 / SU B: 1.851 / SU ML: 0.065 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.126 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 897 4.9 %RANDOM
Rwork0.18407 ---
all0.18733 86002 --
obs0.18733 17388 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 0 151 1179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211061
X-RAY DIFFRACTIONr_bond_other_d0.0020.02937
X-RAY DIFFRACTIONr_angle_refined_deg1.8192.0091439
X-RAY DIFFRACTIONr_angle_other_deg0.93732186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145140
X-RAY DIFFRACTIONr_chiral_restr0.120.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021196
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02209
X-RAY DIFFRACTIONr_nbd_refined0.2160.2234
X-RAY DIFFRACTIONr_nbd_other0.2540.21091
X-RAY DIFFRACTIONr_nbtor_other0.0930.2655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.215
X-RAY DIFFRACTIONr_mcbond_it1.8671.5704
X-RAY DIFFRACTIONr_mcangle_it2.79421120
X-RAY DIFFRACTIONr_scbond_it3.9053357
X-RAY DIFFRACTIONr_scangle_it5.5664.5319
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 56
Rwork0.213 1161

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