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

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Basic information

Entry
Database: PDB / ID: 2dsr
TitleStructural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins
Components
  • (Insulin-like growth factor-binding protein 4) x 2
  • Insulin-like growth factor IB
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 / 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 / lung vasculature development / exocytic vesicle / 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 / 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 / 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 / negative regulation of canonical Wnt signaling pathway / circadian rhythm / hormone activity / negative regulation of ERK1 and ERK2 cascade
Similarity search - Function
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-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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 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
G: Insulin-like growth factor-binding protein 4
B: Insulin-like growth factor-binding protein 4
I: Insulin-like growth factor IB


Theoretical massNumber of molelcules
Total (without water)25,2803
Polymers25,2803
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-29 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.400, 50.250, 64.300
Angle α, β, γ (deg.)90.00, 115.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 9118.353 Da / Num. of mol.: 1 / 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: P22692
#2: 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: 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
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1M lithium sulfate monohydrate, 2% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 13115 / Num. obs: 12370 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.2 Å / % possible all: 68.8

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Processing

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

2dsq


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.881 / SU B: 4.829 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.233 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25641 602 4.9 %RANDOM
Rwork0.19906 ---
obs0.20173 11757 97.72 %-
all-12370 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.537 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.06 Å2
2---0.1 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 0 241 1845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211649
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9882232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29523.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29315251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4411512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021260
X-RAY DIFFRACTIONr_nbd_refined0.1770.2785
X-RAY DIFFRACTIONr_nbtor_refined0.2830.21113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.221
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 40 -
Rwork0.19 652 -
obs--74.33 %

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