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- EMDB-32735: Structure of Human IGF1/IGFBP3/ALS Ternary Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32735
TitleStructure of Human IGF1/IGFBP3/ALS Ternary Complex
Map data
Sample
  • Complex: Ternary complex of IGF1/IGFBP3/ALS
    • Protein or peptide: Insulin-like growth factor-binding protein complex acid labile subunit
    • Protein or peptide: Insulin-like growth factor-binding protein 3
    • Protein or peptide: Isoform 3 of Insulin-like growth factor I
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGrowth / Proliferation / Differentiation / Metabolism / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of insulin-like growth factor receptor signaling pathway / protein tyrosine phosphatase activator activity / 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 ...regulation of insulin-like growth factor receptor signaling pathway / protein tyrosine phosphatase activator activity / 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 / insulin-like growth factor 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 / negative regulation of smooth muscle cell migration / 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 / glial cell differentiation / insulin-like growth factor II binding / 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 / TP53 Regulates Transcription of Death Receptors and Ligands / 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 / negative regulation of protein phosphorylation / positive regulation of activated T cell proliferation / inner ear development / negative regulation of smooth muscle cell apoptotic process / negative regulation of amyloid-beta formation / fibronectin binding / myoblast proliferation / regulation of glucose metabolic process / epithelial to mesenchymal transition / negative regulation of tumor necrosis factor production / Synthesis, secretion, and deacylation of Ghrelin / blood vessel remodeling / activation of protein kinase B activity / positive regulation of glycogen biosynthetic process / positive regulation of myoblast differentiation / positive regulation of osteoblast differentiation / negative regulation of signal transduction / 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 / extracellular matrix / 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 / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / Post-translational protein phosphorylation
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 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 / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / 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 1 / Insulin-like growth factor-binding protein 3 / Insulin-like growth factor-binding protein complex acid labile subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKim H / Fu Y / Kim HM
Funding support1 items
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 HJ / Lee SG / Lee DS / Kim HM
History
DepositionJan 27, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32735.png

Downloads & links

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Map

FileDownload / File: emd_32735.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 300 pix.
= 264.9 Å		0.88 Å/pix.
x 300 pix.
= 264.9 Å		0.88 Å/pix.
x 300 pix.
= 264.9 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.883 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.68561953 - 1.4313762
Average (Standard dev.)-0.0005136444 (±0.0321102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 264.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32735_msk_1.map
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Half map: #2

Fileemd_32735_half_map_1.map
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Half map: #1

Fileemd_32735_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ternary complex of IGF1/IGFBP3/ALS

EntireName: Ternary complex of IGF1/IGFBP3/ALS
Components
  • Complex: Ternary complex of IGF1/IGFBP3/ALS
    • Protein or peptide: Insulin-like growth factor-binding protein complex acid labile subunit
    • Protein or peptide: Insulin-like growth factor-binding protein 3
    • Protein or peptide: Isoform 3 of Insulin-like growth factor I
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of IGF1/IGFBP3/ALS

SupramoleculeName: Ternary complex of IGF1/IGFBP3/ALS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Insulin-like growth factor-binding protein complex acid labile subunit

MacromoleculeName: Insulin-like growth factor-binding protein complex acid labile subunit
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.312316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ADPGTPGEAE GPACPAACVC SYDDDADELS VFCSSRNLTR LPDGVPGGTQ ALWLDGNNLS SVPPAAFQNL SSLGFLNLQG GQLGSLEPQ ALLGLENLCH LHLERNQLRS LALGTFAHTP ALASLGLSNN RLSRLEDGLF EGLGSLWDLN LGWNSLAVLP D AAFRGLGS ...String:
ADPGTPGEAE GPACPAACVC SYDDDADELS VFCSSRNLTR LPDGVPGGTQ ALWLDGNNLS SVPPAAFQNL SSLGFLNLQG GQLGSLEPQ ALLGLENLCH LHLERNQLRS LALGTFAHTP ALASLGLSNN RLSRLEDGLF EGLGSLWDLN LGWNSLAVLP D AAFRGLGS LRELVLAGNR LAYLQPALFS GLAELRELDL SRNALRAIKA NVFVQLPRLQ KLYLDRNLIA AVAPGAFLGL KA LRWLDLS HNRVAGLLED TFPGLLGLRV LRLSHNAIAS LRPRTFKDLH FLEELQLGHN RIRQLAERSF EGLGQLEVLT LDH NQLQEV KAGAFLGLTN VAVMNLSGNC LRNLPEQVFR GLGKLHSLHL EGSCLGRIRP HTFTGLSGLR RLFLKDNGLV GIEE QSLWG LAELLELDLT SNQLTHLPHR LFQGLGKLEY LLLSRNRLAE LPADALGPLQ RAFWLDVSHN RLEALPNSLL APLGR LRYL SLRNNSLRTF TPQPPGLERL WLEGNPWDCG CPLKALRDFA LQNPSAVPRF VQAICEGDDC QPPAYTYNNI TCASPP EVV GLDLRDLSEA HFAPC

UniProtKB: Insulin-like growth factor-binding protein complex acid labile subunit

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Macromolecule #2: Insulin-like growth factor-binding protein 3

MacromoleculeName: Insulin-like growth factor-binding protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.79474 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GASSAGLGPV VRCEPCDARA LAQCAPPPAV CAELVREPGC GCCLTCALSE GQPCGIYTER CGSGLRCQPS PDEARPLQAL LDGRGLCVN ASAVSRLRAY LLPAPPAPGN ASESEEDRSA GSVESPSVSS THRVSDPKFH PLHSKIIIIK KGHAKDSQRY K VDYESQST ...String:
GASSAGLGPV VRCEPCDARA LAQCAPPPAV CAELVREPGC GCCLTCALSE GQPCGIYTER CGSGLRCQPS PDEARPLQAL LDGRGLCVN ASAVSRLRAY LLPAPPAPGN ASESEEDRSA GSVESPSVSS THRVSDPKFH PLHSKIIIIK KGHAKDSQRY K VDYESQST DTQNFSSESK RETEYGPCRR EMEDTLNHLK FLNVLSPRGV HIPNCDKKGF YKKKQCRPSK GRKRGFCWCV DK YGQPLPG YTTKGKEDVH CYSMQSK

UniProtKB: Insulin-like growth factor-binding protein 3

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Macromolecule #3: Isoform 3 of Insulin-like growth factor I

MacromoleculeName: Isoform 3 of Insulin-like growth factor I / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.663752 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GPETLCGAEL VDALQFVCGD RGFYFNKPTG YGSSSRRAPQ TGIVDECCFR SCDLRRLEMY CAPLKPAKSA

UniProtKB: Insulin-like growth factor 1

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
200.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsCDS mode is used
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 14754 / Average exposure time: 3.4 sec. / Average electron dose: 63.23033928 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2dsr


Details: IGF1/IGFBP4 complex (2DSR) is used as an initial model. The structure of ALS is manually built.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 638058
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.1) / Details: Cryosprac
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0.1)
FSC plot (resolution estimation)

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