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- PDB-7yrr: Cryo-EM structure of IGF1R with two IGF1 complex -

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Basic information

Entry
Database: PDB / ID: 7yrr
TitleCryo-EM structure of IGF1R with two IGF1 complex
Components
  • Insulin-like growth factor 1 receptor
  • Isoform 3 of Insulin-like growth factor I
KeywordsMEMBRANE PROTEIN / IGF1R-IGF1
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsXi, Z. / Cang, W.
Funding support1items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin-like growth factor 1 receptor
B: Insulin-like growth factor 1 receptor
C: Isoform 3 of Insulin-like growth factor I
D: Isoform 3 of Insulin-like growth factor I


Theoretical massNumber of molelcules
Total (without water)218,2154
Polymers218,2154
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Insulin-like growth factor 1 receptor / Insulin-like growth factor I receptor / IGF-I receptor


Mass: 102424.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P08069, receptor protein-tyrosine kinase
#2: Protein Isoform 3 of Insulin-like growth factor I / IGF-I / Mechano growth factor / MGF / Somatomedin-C


Mass: 6682.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P05019
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Deterotetramer complex of IGF1R with IGF1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.3 Å / Resolution method: OTHER / Num. of particles: 100000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313819
ELECTRON MICROSCOPYf_angle_d0.61518690
ELECTRON MICROSCOPYf_dihedral_angle_d5.3781842
ELECTRON MICROSCOPYf_chiral_restr0.0432015
ELECTRON MICROSCOPYf_plane_restr0.0062425

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