[English] 日本語
Yorodumi
- PDB-1wqj: Structural Basis for the Regulation of Insulin-Like Growth Factor... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 cardiac muscle hypertrophy / positive regulation of activated T cell proliferation / 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 / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / 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 / insulin-like growth factor receptor binding / activation of protein kinase B activity / positive regulation of glycolytic process / 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 / positive regulation of protein secretion / regulation of cell growth / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of glucose import / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / regulation of protein phosphorylation / 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) / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / 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 growth factor binding protein / Insulin-like, subunit E / Insulin-like ...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 growth factor binding protein / Insulin-like, subunit E / Insulin-like / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more