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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 / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of glycoprotein biosynthetic process / proteoglycan biosynthetic process ...regulation of insulin-like growth factor receptor signaling pathway / protein tyrosine phosphatase activator activity / 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 / positive regulation of glycoprotein biosynthetic process / 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 / 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 / negative regulation of vascular associated smooth muscle cell apoptotic process / exocytic vesicle / cell activation / insulin-like growth factor II binding / 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 / myoblast proliferation / alphav-beta3 integrin-IGF-1-IGF1R complex / cell surface receptor signaling pathway via STAT / myoblast differentiation / 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 / muscle organ development / positive regulation of cardiac muscle hypertrophy / 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 / negative regulation of protein phosphorylation / fibronectin binding / regulation of glucose metabolic process / negative regulation of tumor necrosis factor production / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / positive regulation of myoblast differentiation / activation of protein kinase B activity / positive regulation of glycogen biosynthetic process / SHC-related events triggered by IGF1R / positive regulation of osteoblast differentiation / negative regulation of signal transduction / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / extracellular matrix / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / positive regulation of epithelial cell proliferation / positive regulation of glycolytic process / 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 / regulation of cell growth / positive regulation of smooth muscle cell proliferation / negative regulation of smooth muscle cell proliferation / growth factor activity / wound healing / hormone activity / positive regulation of fibroblast proliferation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / osteoblast differentiation / integrin binding / MAPK cascade / insulin receptor signaling pathway / Platelet degranulation / response to heat / regulation of gene expression / Ras protein signal transduction / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of MAPK cascade / protein stabilization / positive regulation of cell migration / protein phosphorylation / positive regulation of apoptotic process / endoplasmic reticulum lumen / negative regulation of cell population proliferation / negative regulation of gene expression
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

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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
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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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