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- EMDB-34065: Cryo-EM structure of IGF1R with two IGF1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-34065
TitleCryo-EM structure of IGF1R with two IGF1 complex
Map data
Sample
  • Complex: Deterotetramer complex of IGF1R with IGF1
    • Protein or peptide: Insulin-like growth factor 1 receptor
    • Protein or peptide: Isoform 3 of Insulin-like growth factor I
KeywordsIGF1R-IGF1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / cardiac atrium development / negative regulation of cholangiocyte apoptotic process / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process ...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 / cardiac atrium development / negative regulation of cholangiocyte apoptotic process / proteoglycan biosynthetic process / positive regulation of glycoprotein biosynthetic process / myotube cell development / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / 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 / protein transporter activity / positive regulation of cell growth involved in cardiac muscle cell development / exocytic vesicle / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of transcription regulatory region DNA binding / positive regulation of DNA metabolic process / cellular response to aldosterone / cellular response to zinc ion starvation / cell activation / positive regulation of calcineurin-NFAT signaling cascade / insulin receptor complex / insulin-like growth factor I binding / cellular response to testosterone stimulus / transcytosis / insulin receptor activity / negative regulation of hepatocyte apoptotic process / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / cellular response to angiotensin / positive regulation of Ras protein signal transduction / positive regulation of protein-containing complex disassembly / myoblast differentiation / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / dendritic spine maintenance / insulin binding / negative regulation of interleukin-1 beta production / response to L-glutamate / cellular response to insulin-like growth factor stimulus / muscle organ development / positive regulation of DNA binding / establishment of cell polarity / negative regulation of release of cytochrome c from mitochondria / positive regulation of cytokinesis / positive regulation of cardiac muscle hypertrophy / positive regulation of axon regeneration / positive regulation of smooth muscle cell migration / positive regulation of activated T cell proliferation / positive regulation of osteoblast proliferation / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / amyloid-beta clearance / regulation of JNK cascade / Respiratory syncytial virus (RSV) attachment and entry / negative regulation of tumor necrosis factor production / insulin receptor substrate binding / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / G-protein alpha-subunit binding / Synthesis, secretion, and deacylation of Ghrelin / response to vitamin E / estrous cycle / negative regulation of MAPK cascade / SHC-related events triggered by IGF1R / positive regulation of osteoblast differentiation / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to transforming growth factor beta stimulus / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / T-tubule / activation of protein kinase B activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / axonogenesis / cellular response to dexamethasone stimulus / cerebellum development / positive regulation of epithelial cell proliferation / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / skeletal system development / hippocampus development / cellular response to estradiol stimulus / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of extrinsic apoptotic signaling pathway
Similarity search - Function
Insulin-like growth factor I / Insulin-like growth factor / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site ...Insulin-like growth factor I / Insulin-like growth factor / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Insulin-like growth factor I / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsXi Z / Cang W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of IGF1R with two IGF1 complex at 4.3 angstroms resolution
Authors: Xi Z / Cang W
History
DepositionAug 10, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34065.png

Downloads & links

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Map

FileDownload / File: emd_34065.map.gz / Format: CCP4 / Size: 178 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.)
0.83 Å/pix.
x 360 pix.
= 297.72 Å		0.83 Å/pix.
x 360 pix.
= 297.72 Å		0.83 Å/pix.
x 360 pix.
= 297.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.062
Minimum - Maximum-0.42119583 - 0.66601026
Average (Standard dev.)0.00014640341 (±0.012107538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34065_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34065_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Deterotetramer complex of IGF1R with IGF1

EntireName: Deterotetramer complex of IGF1R with IGF1
Components
  • Complex: Deterotetramer complex of IGF1R with IGF1
    • Protein or peptide: Insulin-like growth factor 1 receptor
    • Protein or peptide: Isoform 3 of Insulin-like growth factor I

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Supramolecule #1: Deterotetramer complex of IGF1R with IGF1

SupramoleculeName: Deterotetramer complex of IGF1R with IGF1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Insulin-like growth factor 1 receptor

MacromoleculeName: Insulin-like growth factor 1 receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.424906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFRV AGLESLGDLF PNLTVIRGWK LFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL ILDAVSNNYI VGNKPPKECG DLCPGTMEEK P MCEKTTIN ...String:
EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFRV AGLESLGDLF PNLTVIRGWK LFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL ILDAVSNNYI VGNKPPKECG DLCPGTMEEK P MCEKTTIN NEYNYRCWTT NRCQKMCPST CGKRACTENN ECCHPECLGS CSAPDNDTAC VACRHYYYAG VCVPACPPNT YR FEGWRCV DRDFCANILS AESSDSEGFV IHDGECMQEC PSGFIRNGSQ SMYCIPCEGP CPKVCEEEKK TKTIDSVTSA QML QGCTIF KGNLLINIRR GNNIASELEN FMGLIEVVTG YVKIRHSHAL VSLSFLKNLR LILGEEQLEG NYSFYVLDNQ NLQQ LWDWD HRNLTIKAGK MYFAFNPKLC VSEIYRMEEV TGTKGRQSKG DINTRNNGER ASCESDVLHF TSTTTSKNRI IITWH RYRP PDYRDLISFT VYYKEAPFKN VTEYDGQDAC GSNSWNMVDV DLPPNKDVEP GILLHGLKPW TQYAVYVKAV TLTMVE NDH IRGAKSEILY IRTNASVPSI PLDVLSASNS SSQLIVKWNP PSLPNGNLSY YIVRWQRQPQ DGYLYRHNYC SKDKIPI RK YADGTIDIEE VTENPKTEVC GGEKGPCCAC PKTEAEKQAE KEEAEYRKVF ENFLHNSIFV PRPERKRRDV MQVANTTM S SRSRNTTAAD TYNITDPEEL ETEYPFFESR VDNKERTVIS NLRPFTLYRI DIHSCNHEAE KLGCSASNFV FARTMPAEG ADDIPGPVTW EPRPENSIFL KWPEPENPNG LILMYEIKYG SQVEDQRECV SRQEYRKYGG AKLNRLNPGN YTARIQATSL SGNGSWTDP VFFYVQAK

UniProtKB: Insulin-like growth factor 1 receptor

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Macromolecule #2: Isoform 3 of Insulin-like growth factor I

MacromoleculeName: Isoform 3 of Insulin-like growth factor I / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.682607 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TLCGAELVDA LQFVCGDRGF YFNKPTGYGS SSRRAPQTGI VDECCFRSCD LRRLEMYCAP

UniProtKB: Insulin-like growth factor I

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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

BufferpH: 7.4
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Number images used: 100000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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