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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
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 / myoblast proliferation / positive regulation of insulin-like growth factor receptor signaling pathway / muscle organ development / TP53 Regulates Transcription of Death Receptors and Ligands / negative regulation of interleukin-1 beta production / 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 / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / positive regulation of myoblast differentiation / positive regulation of osteoblast differentiation / positive regulation of DNA binding / SHC-related events triggered by IGF1R / 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 / extracellular matrix / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / 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 / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / 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 / 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 fibroblast proliferation / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / 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 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 / protein phosphorylation / negative regulation of gene expression / 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)
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-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing 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)
Voxel sizeX=Y=Z: 0.883 Å
Density
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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32735_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_32735_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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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 / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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

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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

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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

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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 / N-Acetylglucosamine

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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 chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
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
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.
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)
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
FSC plot (resolution estimation)

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