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- PDB-1h59: Complex of IGFBP-5 with IGF-I -

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Basic information

Entry
Database: PDB / ID: 1h59
TitleComplex of IGFBP-5 with IGF-I
Components
  • INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5
  • INSULIN-LIKE GROWTH FACTOR IA
KeywordsINSULIN / INSULIN-LIKE GROWTH FACTOR / IGF BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of muscle tissue development / negative regulation of skeletal muscle hypertrophy / regulation of insulin-like growth factor receptor signaling pathway / prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / type II pneumocyte differentiation / neuronal dense core vesicle lumen / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development ...negative regulation of muscle tissue development / negative regulation of skeletal muscle hypertrophy / regulation of insulin-like growth factor receptor signaling pathway / prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / type II pneumocyte differentiation / neuronal dense core vesicle lumen / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / regulation of establishment or maintenance of cell polarity / positive regulation of trophectodermal cell proliferation / positive regulation of glycoprotein biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / negative regulation of insulin-like growth factor receptor signaling pathway / proteoglycan biosynthetic process / myotube cell development / positive regulation of transcription regulatory region DNA binding / mammary gland involution / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of neuroinflammatory response / negative regulation of growth / lung vasculature development / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of smooth muscle cell migration / bone mineralization involved in bone maturation / positive regulation of cell growth involved in cardiac muscle cell development / IRS-related events triggered by IGF1R / cerebellar granule cell precursor proliferation / negative regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of myoblast proliferation / exocytic vesicle / lung lobe morphogenesis / positive regulation of myelination / negative regulation of androgen receptor signaling pathway / glial cell differentiation / cell activation / insulin-like growth factor II binding / prostate gland growth / positive regulation of calcineurin-NFAT signaling cascade / type B pancreatic cell proliferation / transmembrane receptor protein tyrosine kinase activator activity / insulin-like growth factor I binding / mammary gland development / exocrine pancreas development / alphav-beta3 integrin-IGF-1-IGF1R complex / regulation of nitric oxide biosynthetic process / positive regulation of vascular associated smooth muscle cell migration / myoblast differentiation / cell surface receptor signaling pathway via STAT / response to growth hormone / 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 / hair follicle morphogenesis / muscle organ development / branching morphogenesis of an epithelial tube / positive regulation of cardiac muscle hypertrophy / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / type I pneumocyte differentiation / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / positive regulation of activated T cell proliferation / inner ear development / androgen receptor signaling pathway / fibronectin binding / myoblast proliferation / blood vessel remodeling / negative regulation of tumor necrosis factor production / epithelial to mesenchymal transition / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of osteoblast differentiation / activation of protein kinase B activity / positive regulation of glycogen biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of osteoblast differentiation / SHC-related events triggered by IGF1R / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / cellular response to cAMP / extrinsic apoptotic signaling pathway in absence of ligand / striated muscle cell differentiation / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / negative regulation of cell migration / positive regulation of epithelial cell proliferation / platelet alpha granule lumen / positive regulation of glycolytic process / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion
Similarity search - Function
Insulin-like growth factor binding protein 5 / 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 5 / 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 1 / Insulin-like growth factor-binding protein 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.1 Å
AuthorsZeslawski, W. / Beisel, H.G. / Kamionka, M. / Kalus, W. / Engh, R.A. / Huber, R. / Holak, T.A.
CitationJournal: Embo J. / Year: 2001
Title: The Interaction of Insulin-Like Growth Factor-I with the N-Terminal Domain of Igfbp-5
Authors: Zesaawski, W. / Beisel, H.G. / Kamionka, M. / Kalus, W. / Engh, R.A. / Huber, R. / Lang, K. / Holak, T.A.
History
DepositionMay 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN-LIKE GROWTH FACTOR IA
B: INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5


Theoretical massNumber of molelcules
Total (without water)13,7162
Polymers13,7162
Non-polymers00
Water79344
1
A: INSULIN-LIKE GROWTH FACTOR IA
B: INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5

A: INSULIN-LIKE GROWTH FACTOR IA
B: INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5

A: INSULIN-LIKE GROWTH FACTOR IA
B: INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5


Theoretical massNumber of molelcules
Total (without water)41,1476
Polymers41,1476
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
MethodPQS
Unit cell
Length a, b, c (Å)74.385, 74.385, 74.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

DetailsTRIMER OF THE HETERODIMERIC COMPLEX OF IGF- IA AND IGFBP-5

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Components

#1: Protein INSULIN-LIKE GROWTH FACTOR IA / IGF-I / IGF-IA / SOMATOMEDIN C


Mass: 7663.752 Da / Num. of mol.: 1 / Fragment: RESIDUES 49-118 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01343, UniProt: P05019*PLUS
#2: Protein INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN 5 / IGFBP-5 / IBP-5 / IGF-BINDING PROTEIN 5


Mass: 6051.915 Da / Num. of mol.: 1 / Fragment: N-TERMINAL IGF BINDING DOMAIN RESIDUE 58-111 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P24593
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %Jeffamine M-60011
20.1 Msodium citrate11
30.01 M11pH5.6FeCl

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→16.2 Å / Num. obs: 8035 / % possible obs: 96.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 2.11→2.23 Å / Rmerge(I) obs: 0.448 / % possible all: 96.9
Reflection
*PLUS
% possible obs: 99.3 % / Num. measured all: 45345
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIR / Resolution: 2.1→16.2 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 501 6 %RANDOM
Rwork0.218 ---
obs0.218 8023 99.3 %-
Refinement stepCycle: LAST / Resolution: 2.1→16.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 0 0 44 809
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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