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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 / proteoglycan biosynthetic process / negative regulation of smooth muscle cell migration ...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 / 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 / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / negative regulation of vascular associated smooth muscle cell apoptotic process / bone mineralization involved in bone maturation / insulin-like growth factor binding / IRS-related events triggered by IGF1R / positive regulation of cell growth involved in cardiac muscle cell development / exocytic vesicle / positive regulation of transcription regulatory region DNA binding / cell activation / insulin-like growth factor II binding / positive regulation of calcineurin-NFAT signaling cascade / type B pancreatic cell proliferation / 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 / TP53 Regulates Transcription of Death Receptors and Ligands / muscle organ development / negative regulation of interleukin-1 beta production / positive regulation of DNA binding / negative regulation of release of cytochrome c from mitochondria / positive regulation of cardiac muscle hypertrophy / positive regulation of smooth muscle cell migration / positive regulation of activated T cell proliferation / 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 / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of myoblast differentiation / 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 / insulin-like growth factor receptor binding / activation of protein kinase B activity / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / extracellular matrix / negative regulation of protein phosphorylation / positive regulation of epithelial cell proliferation / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of extrinsic apoptotic signaling pathway / regulation of cell growth / Post-translational protein phosphorylation / negative regulation of smooth muscle cell proliferation / positive regulation of smooth muscle cell proliferation / insulin receptor binding / growth factor activity / wound healing / regulation of protein phosphorylation / hormone activity / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / MAPK cascade / integrin binding / Platelet degranulation / response to heat / regulation of gene expression / Ras protein signal transduction / cell population proliferation / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / protein phosphorylation / negative regulation of cell population proliferation / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of cell population proliferation
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 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine Rich Repeat / 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 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)
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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Others
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 I

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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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