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- PDB-7wrq: Structure of Human IGF1/IGFBP3/ALS Ternary Complex -

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Basic information

Entry
Database: PDB / ID: 7wrq
TitleStructure of Human IGF1/IGFBP3/ALS Ternary Complex
Components
  • Insulin-like growth factor-binding protein 3
  • Insulin-like growth factor-binding protein complex acid labile subunit
  • Isoform 3 of Insulin-like growth factor I
KeywordsSIGNALING PROTEIN / Growth / Proliferation / Differentiation / Metabolism
Function / homology
Function and homology information


protein tyrosine phosphatase activator activity / 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 / negative regulation of smooth muscle cell migration ...protein tyrosine phosphatase activator activity / 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 / negative regulation of smooth muscle cell migration / 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 / insulin-like growth factor binding / 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 / TP53 Regulates Transcription of Death Receptors and Ligands / 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 / fibronectin binding / 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 myoblast differentiation / positive regulation of DNA binding / SHC-related events triggered by IGF1R / positive regulation of osteoblast differentiation / negative regulation of signal transduction / 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 / extracellular matrix / negative regulation of protein phosphorylation / 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 / negative regulation of smooth muscle cell proliferation / 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 / hormone activity / osteoblast differentiation / 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 / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / endoplasmic reticulum lumen / negative regulation of gene expression / protein phosphorylation / apoptotic process
Similarity search - Function
Insulin-like growth factor binding protein 3 / 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. / 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 ...Insulin-like growth factor binding protein 3 / 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. / 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. / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Growth factor receptor cysteine-rich domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Insulin-like growth factor I / Insulin-like growth factor-binding protein 3 / Insulin-like growth factor-binding protein complex acid labile subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKim, H. / Fu, Y. / Kim, H.M.
Funding support1items
OrganizationGrant numberCountry
Other governmentInstiture of Basic Science, IBS-R030-C1
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for assembly and disassembly of the IGF/IGFBP/ALS ternary complex
Authors: Kim, H. / Fu, Y. / Hong, H.J. / Lee, S.G. / Lee, D.S. / Kim, H.M.
History
DepositionJan 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-like growth factor-binding protein complex acid labile subunit
B: Insulin-like growth factor-binding protein 3
C: Isoform 3 of Insulin-like growth factor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2428
Polymers99,7713
Non-polymers1,4715
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, co-Expressed and purified
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Insulin-like growth factor-binding protein complex acid labile subunit / ALS


Mass: 63312.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALS / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P35858
#2: Protein Insulin-like growth factor-binding protein 3 / IBP-3 / IGF-binding protein 3 / IGFBP-3


Mass: 28794.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGFBP3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P17936
#3: Protein Isoform 3 of Insulin-like growth factor I / IGF-I / Mechano growth factor / MGF / Somatomedin-C


Mass: 7663.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P05019
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of IGF1/IGFBP3/ALS / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris1
2200 mMsodium chlorideNaCl1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: CDS mode is used
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3.4 sec. / Electron dose: 63.23033928 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14754

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Processing

EM software
IDNameVersionCategory
10cryoSPARC3.0.1initial Euler assignment
11cryoSPARC3.0.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 638058 / Num. of class averages: 1 / Symmetry type: POINT

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