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- EMDB-38420: Cryo-EM structure of human insulin receptor bound to 4 IGF-I, con... -

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Basic information

Entry
Database: EMDB / ID: EMD-38420
TitleCryo-EM structure of human insulin receptor bound to 4 IGF-I, conformation 3
Map data
Sample
  • Complex: The complex of insulin receptor with 4 IGF-I
    • Protein or peptide: Isoform Short of Insulin receptor
    • Protein or peptide: Insulin-like growth factor I
KeywordsMEMBRANE 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 / positive regulation of glycoprotein biosynthetic process / proteoglycan biosynthetic process / myotube cell development / negative regulation of neuroinflammatory response ...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 / negative regulation of neuroinflammatory response / positive regulation of transcription regulatory region DNA 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 / 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 / regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / cell activation / positive regulation of developmental growth / positive regulation of calcineurin-NFAT signaling cascade / male sex determination / insulin receptor complex / transmembrane receptor protein tyrosine kinase activator activity / insulin-like growth factor I binding / exocrine pancreas development / positive regulation of protein-containing complex disassembly / 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 / dendritic spine maintenance / myoblast proliferation / cargo receptor activity / insulin binding / growth hormone receptor signaling pathway / negative regulation of interleukin-1 beta production / positive regulation of DNA binding / neuronal cell body membrane / adrenal gland development / PTB domain binding / muscle organ development / Signaling by Insulin receptor / positive regulation of smooth muscle cell migration / IRS activation / 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 / positive regulation of respiratory burst / amyloid-beta clearance / regulation of embryonic development / positive regulation of receptor internalization / protein kinase activator activity / insulin receptor substrate binding / negative regulation of tumor necrosis factor production / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / Signal attenuation / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / positive regulation of osteoblast differentiation / transport across blood-brain barrier / heart morphogenesis / activation of protein kinase B activity / positive regulation of vascular associated smooth muscle cell proliferation / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / positive regulation of MAP kinase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / positive regulation of glycolytic process / positive regulation of epithelial cell proliferation / learning / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of smooth muscle cell proliferation / insulin receptor binding / growth factor activity / wound healing / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity
Similarity search - Function
Insulin-like growth factor I / Insulin-like growth factor / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / 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-like growth factor I / Insulin-like growth factor / Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / 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 III domain / : / 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 1 / Insulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsXi Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of human insulin receptor bound to 4 IGF-I, conformation 3
Authors: Xi Z
History
DepositionDec 23, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38420.png

Downloads & links

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Map

FileDownload / File: emd_38420.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.10404328 - 0.2380038
Average (Standard dev.)0.000039468105 (±0.0052064513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38420_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_38420_half_map_1.map
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Histogram

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Half map: #1

Fileemd_38420_half_map_2.map
Projections & Slices
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Sample components

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Entire : The complex of insulin receptor with 4 IGF-I

EntireName: The complex of insulin receptor with 4 IGF-I
Components
  • Complex: The complex of insulin receptor with 4 IGF-I
    • Protein or peptide: Isoform Short of Insulin receptor
    • Protein or peptide: Insulin-like growth factor I

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Supramolecule #1: The complex of insulin receptor with 4 IGF-I

SupramoleculeName: The complex of insulin receptor with 4 IGF-I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform Short of Insulin receptor

MacromoleculeName: Isoform Short of Insulin receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 155.329094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATGGRRGAA AAPLLVAVAA LLLGAAGHLY PGEVCPGMDI RNNLTRLHEL ENCSVIEGHL QILLMFKTRP EDFRDLSFPK LIMITDYLL LFRVYGLESL KDLFPNLTVI RGSRLFFNYA LVIFEMVHLK ELGLYNLMNI TRGSVRIEKN NELCYLATID W SRILDSVE ...String:
MATGGRRGAA AAPLLVAVAA LLLGAAGHLY PGEVCPGMDI RNNLTRLHEL ENCSVIEGHL QILLMFKTRP EDFRDLSFPK LIMITDYLL LFRVYGLESL KDLFPNLTVI RGSRLFFNYA LVIFEMVHLK ELGLYNLMNI TRGSVRIEKN NELCYLATID W SRILDSVE DNYIVLNKDD NEECGDICPG TAKGKTNCPA TVINGQFVER CWTHSHCQKV CPTICKSHGC TAEGLCCHSE CL GNCSQPD DPTKCVACRN FYLDGRCVET CPPPYYHFQD WRCVNFSFCQ DLHHKCKNSR RQGCHQYVIH NNKCIPECPS GYT MNSSNL LCTPCLGPCP KVCHLLEGEK TIDSVTSAQE LRGCTVINGS LIINIRGGNN LAAELEANLG LIEEISGYLK IRRS YALVS LSFFRKLRLI RGETLEIGNY SFYALDNQNL RQLWDWSKHN LTITQGKLFF HYNPKLCLSE IHKMEEVSGT KGRQE RNDI ALKTNGDQAS CENELLKFSY IRTSFDKILL RWEPYWPPDF RDLLGFMLFY KEAPYQNVTE FDGQDACGSN SWTVVD IDP PLRSNDPKSQ NHPGWLMRGL KPWTQYAIFV KTLVTFSDER RTYGAKSDII YVQTDATNPS VPLDPISVSN SSSQIIL KW KPPSDPNGNI THYLVFWERQ AEDSELFELD YCLKGLKLPS RTWSPPFESE DSQKHNQSEY EDSAGECCSC PKTDSQIL K ELEESSFRKT FEDYLHNVVF VPRPSRKRRS LGDVGNVTVA VPTVAAFPNT SSTSVPTSPE EHRPFEKVVN KESLVISGL RHFTGYRIEL QACNQDTPEE RCSVAAYVSA RTMPEAKADD IVGPVTHEIF ENNVVHLMWQ EPKEPNGLIV LYEVSYRRYG DEELHLCVS RKHFALERGC RLRGLSPGNY SVRIRATSLA GNGSWTEPTY FYVTDYLDVP SNIAKIIIGP LIFVFLFSVV I GSIYLFLR KRQPDGPLGP LYASSNPEYL SASDVFPCSV YVPDEWEVSR EKITLLRELG QGSFGMVYEG NARDIIKGEA ET RVAVKTV NESASLRERI EFLNEASVMK GFTCHHVVRL LGVVSKGQPT LVVMELMAHG DLKSYLRSLR PEAENNPGRP PPT LQEMIQ MAAEIADGMA YLNAKKFVHR DLAARNCMVA HDFTVKIGDF GMTRDIYETD YYRKGGKGLL PVRWMAPESL KDGV FTTSS DMWSFGVVLW EITSLAEQPY QGLSNEQVLK FVMDGGYLDQ PDNCPERVTD LMRMCWQFNP KMRPTFLEIV NLLKD DLHP SFPEVSFFHS EENKAPESEE LEMEFEDMEN VPLDRSSHCQ REEAGGRDGG SSLGFKRSYE EHIPYTHMNG GKKNGR ILT LPRSNPS

UniProtKB: Insulin receptor

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Macromolecule #2: Insulin-like growth factor I

MacromoleculeName: Insulin-like growth factor I / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.88132 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGKISSLPTQ LFKCCFCDFL KVKMHTMSSS HLFYLALCLL TFTSSATAGP ETLCGAELVD ALQFVCGDRG FYFNKPTGYG SSSRRAPQT GIVDECCFRS CDLRRLEMYC APLKPAKSAR SVRAQRHTDM PKTQKYQPPS TNKNTKSQRR KGWPKTHPGG E QKEGTEAS ...String:
MGKISSLPTQ LFKCCFCDFL KVKMHTMSSS HLFYLALCLL TFTSSATAGP ETLCGAELVD ALQFVCGDRG FYFNKPTGYG SSSRRAPQT GIVDECCFRS CDLRRLEMYC APLKPAKSAR SVRAQRHTDM PKTQKYQPPS TNKNTKSQRR KGWPKTHPGG E QKEGTEAS LQIRGKKKEQ RREIGSRNAE CRGKKGK

UniProtKB: Insulin-like growth factor 1

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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: ETHANE

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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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82568
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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