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- PDB-9pvo: Novel site 1 interaction of the IR/Ins-AC-S2 complex -

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Basic information

Entry
Database: PDB / ID: 9pvo
TitleNovel site 1 interaction of the IR/Ins-AC-S2 complex
Components
  • Insulin chain A
  • Insulin chain B
  • Isoform Long of Insulin receptor
KeywordsMEMBRANE PROTEIN / Antagonism / receptor tyrosine kinase
Function / homology
Function and homology information


regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / exocrine pancreas development ...regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / male sex determination / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / exocrine pancreas development / dendritic spine maintenance / insulin binding / adrenal gland development / cargo receptor activity / negative regulation of glycogen catabolic process / : / negative regulation of fatty acid metabolic process / PTB domain binding / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / neuronal cell body membrane / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / positive regulation of respiratory burst / alpha-beta T cell activation / amyloid-beta clearance / regulation of embryonic development / insulin receptor substrate binding / positive regulation of receptor internalization / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / negative regulation of gluconeogenesis / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of insulin receptor signaling pathway / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / protein kinase activator activity / negative regulation of respiratory burst involved in inflammatory response / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / nitric oxide-cGMP-mediated signaling / transport across blood-brain barrier / regulation of protein localization to plasma membrane / positive regulation of nitric-oxide synthase activity / phosphatidylinositol 3-kinase binding / heart morphogenesis / transport vesicle / Insulin receptor recycling / COPI-mediated anterograde transport / positive regulation of brown fat cell differentiation / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / positive regulation of mitotic nuclear division / endoplasmic reticulum-Golgi intermediate compartment membrane / Insulin receptor signalling cascade / receptor-mediated endocytosis / dendrite membrane / positive regulation of glycolytic process / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / positive regulation of long-term synaptic potentiation / learning / positive regulation of protein secretion / positive regulation of cell differentiation / wound healing / Regulation of insulin secretion / hormone activity / receptor protein-tyrosine kinase / positive regulation of neuron projection development / negative regulation of protein catabolic process / caveola / receptor internalization / positive regulation of protein localization to nucleus / regulation of synaptic plasticity / Golgi lumen / male gonad development / cellular response to growth factor stimulus / cognition / vasodilation / glucose metabolic process / cellular response to insulin stimulus / memory / positive regulation of nitric oxide biosynthetic process / insulin receptor signaling pathway / protein autophosphorylation / late endosome / cell-cell signaling
Similarity search - Function
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 / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. ...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 / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Insulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsVogel, A. / Blakely, A. / Hill, C.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK127268 United States
CitationJournal: To Be Published
Title: Structural basis of insulin receptor antagonism by site 1-site 2 ligands
Authors: Vogel, A. / Blakely, A. / Dao, Y. / Lin, N.P. / Chou, D. / Hill, C.P.
History
DepositionAug 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform Long of Insulin receptor
B: Isoform Long of Insulin receptor
Q: Insulin chain A
R: Insulin chain B


Theoretical massNumber of molelcules
Total (without water)227,8084
Polymers227,8084
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform Long of Insulin receptor / IR


Mass: 109477.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Homo sapiens (human)
References: UniProt: P06213, receptor protein-tyrosine kinase
#2: Protein Insulin chain A


Mass: 5520.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein/peptide Insulin chain B


Mass: 3332.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
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: Half model of the insulin receptor-A isoform complexed with Ins-AC-S2.
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212201 / Symmetry type: POINT

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