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- PDB-7s0q: Head region of a complex of IGF-I with the ectodomain of a hybrid... -

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Basic information

Entry
Database: PDB / ID: 7s0q
TitleHead region of a complex of IGF-I with the ectodomain of a hybrid insulin receptor / type 1 insulin-like growth factor receptor
Components
  • (Insulin-like growth factor ...) x 2
  • Insulin receptor
KeywordsSIGNALING PROTEIN / insulin receptor / type 1 insulin like growth factor receptor / hybrid receptor / insulin like growth factor I / leucine zipper / cryo electron microscopy
Function / homology
Function and homology information


glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of trophectodermal cell proliferation / prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / positive regulation of glycoprotein biosynthetic process / type II pneumocyte differentiation ...glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / positive regulation of trophectodermal cell proliferation / prostate gland stromal morphogenesis / positive regulation of type B pancreatic cell proliferation / positive regulation of glycoprotein biosynthetic process / type II pneumocyte differentiation / neuronal dense core vesicle lumen / proteoglycan biosynthetic process / regulation of establishment or maintenance of cell polarity / chondroitin sulfate proteoglycan biosynthetic process / protein kinase complex / insulin-like growth factor receptor activity / myotube cell development / positive regulation of transcription regulatory region DNA binding / negative regulation of neuroinflammatory response / insulin-like growth factor 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 / protein transporter activity / 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 / positive regulation of cerebellar granule cell precursor proliferation / lung vasculature development / exocytic vesicle / transcytosis / cerebellar granule cell precursor proliferation / regulation of female gonad development / positive regulation of myoblast proliferation / positive regulation of meiotic cell cycle / lung lobe morphogenesis / positive regulation of myelination / negative regulation of androgen receptor signaling pathway / cell activation / glial cell differentiation / insulin-like growth factor II binding / positive regulation of developmental growth / positive regulation of calcineurin-NFAT signaling cascade / prostate gland growth / male sex determination / transmembrane receptor protein tyrosine kinase activator activity / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly / type B pancreatic cell proliferation / insulin receptor activity / mammary gland development / exocrine pancreas development / alphav-beta3 integrin-IGF-1-IGF1R complex / myoblast differentiation / cell surface receptor signaling pathway via STAT / regulation of nitric oxide biosynthetic process / positive regulation of Ras protein signal transduction / positive regulation of insulin-like growth factor receptor signaling pathway / regulation of JNK cascade / dendritic spine maintenance / cargo receptor activity / peptidyl-tyrosine autophosphorylation / positive regulation of smooth muscle cell migration / growth hormone receptor signaling pathway / positive regulation of DNA binding / insulin binding / adrenal gland development / negative regulation of interleukin-1 beta production / neuronal cell body membrane / PTB domain binding / lung alveolus development / muscle organ development / Signaling by Insulin receptor / cellular response to insulin-like growth factor stimulus / IRS activation / positive regulation of cardiac muscle hypertrophy / branching morphogenesis of an epithelial tube / androgen receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / negative regulation of release of cytochrome c from mitochondria / type I pneumocyte differentiation / positive regulation of activated T cell proliferation / positive regulation of respiratory burst / amyloid-beta clearance / inner ear development / negative regulation of smooth muscle cell apoptotic process / negative regulation of amyloid-beta formation / Respiratory syncytial virus (RSV) attachment and entry / myoblast proliferation / positive regulation of receptor internalization / regulation of embryonic development / insulin receptor substrate binding / epithelial to mesenchymal transition / negative regulation of tumor necrosis factor production / Synthesis, secretion, and deacylation of Ghrelin / blood vessel remodeling / protein kinase activator activity / activation of protein kinase B activity / epidermis development
Similarity search - Function
Insulin-like growth factor I / Insulin-like growth factor / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / 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. / Alpha-Beta Horseshoe ...Insulin-like growth factor I / Insulin-like growth factor / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / 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. / Alpha-Beta Horseshoe / 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 / Fibronectin type III domain / 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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Insulin-like growth factor 1 / Insulin receptor / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsXu, Y. / Lawrence, M.C.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1128553 Australia
CitationJournal: Structure / Year: 2022
Title: How insulin-like growth factor I binds to a hybrid insulin receptor type 1 insulin-like growth factor receptor.
Authors: Yibin Xu / Mai B Margetts / Hari Venugopal / John G Menting / Nicholas S Kirk / Tristan I Croll / Carlie Delaine / Briony E Forbes / Michael C Lawrence /
Abstract: Monomers of the insulin receptor and type 1 insulin-like growth factor receptor (IGF-1R) can combine stochastically to form heterodimeric hybrid receptors. These hybrid receptors display ligand ...Monomers of the insulin receptor and type 1 insulin-like growth factor receptor (IGF-1R) can combine stochastically to form heterodimeric hybrid receptors. These hybrid receptors display ligand binding and signaling properties that differ from those of the homodimeric receptors. Here, we describe the cryoelectron microscopy structure of such a hybrid receptor in complex with insulin-like growth factor I (IGF-I). The structure (ca. 3.7 Å resolution) displays a single IGF-I ligand, bound in a similar fashion to that seen for IGFs in complex with IGF-1R. The IGF-I ligand engages the first leucine-rich-repeat domain and cysteine-rich region of the IGF-1R monomer (rather than those of the insulin receptor monomer), consistent with the determinants for IGF binding residing in the IGF-1R cysteine-rich region. The structure broadens our understanding of this receptor family and assists in delineating the key structural motifs involved in binding their respective ligands.
History
DepositionAug 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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 receptor
D: Insulin-like growth factor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,73714
Polymers226,4113
Non-polymers3,32611
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11040 Å2
ΔGint12 kcal/mol
Surface area46000 Å2

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Components

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Insulin-like growth factor ... , 2 types, 2 molecules AD

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


Mass: 108937.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Cell line (production host): CHO Lec8 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P08069, receptor protein-tyrosine kinase
#3: Protein Insulin-like growth factor I / IGF-I / Mechano growth factor / MGF / Somatomedin-C


Mass: 7663.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1, IBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05019

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Protein , 1 types, 1 molecules B

#2: Protein Insulin receptor / IR


Mass: 109809.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Cell line (production host): CHO lek8 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P06213, receptor protein-tyrosine kinase

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Sugars , 4 types, 11 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
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: a complex of IGF-I with the ectodomain of a hybrid insulin receptor / type 1 insulin-like growth factor receptor
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 250 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 8 / Details: 20mM Tris pH 8.0 160mM NaCl
Buffer componentConc.: 20 mM / Name: TRIS / Formula: C4H11NO3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.2mg/ml
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17_3644: / Classification: refinement
EM software
IDNameVersionCategory
4cryoSPARC2.15.0CTF correction
7UCSF Chimera1.14model fitting
8PHENIX1.17-3644model fitting
12cryoSPARC2.15.0classification
13cryoSPARC2.15.03D reconstruction
14PHENIX1.17-3644model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151240 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038060
ELECTRON MICROSCOPYf_angle_d0.47210912
ELECTRON MICROSCOPYf_dihedral_angle_d7.5221164
ELECTRON MICROSCOPYf_chiral_restr0.0421228
ELECTRON MICROSCOPYf_plane_restr0.0021387

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