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- PDB-7pg4: Low resolution Cryo-EM structure of the full-length insulin recep... -

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Basic information

Entry
Database: PDB / ID: 7pg4
TitleLow resolution Cryo-EM structure of the full-length insulin receptor bound to 2 insulin, conf 3
Components
  • (Insulin) x 2
  • Isoform Short of Insulin receptor
KeywordsMEMBRANE PROTEIN / Insulin / Receptor / Complex
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 / : / PTB domain binding / negative regulation of fatty acid metabolic process / 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 / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / amyloid-beta clearance / regulation of embryonic development / positive regulation of receptor internalization / insulin receptor substrate binding / 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 / phosphatidylinositol 3-kinase binding / heart morphogenesis / regulation of protein localization to plasma membrane / positive regulation of nitric-oxide synthase activity / transport vesicle / Insulin receptor recycling / COPI-mediated anterograde transport / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / dendrite membrane / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / 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 / receptor internalization / regulation of synaptic plasticity / caveola / positive regulation of protein localization to nucleus / 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: 9.1 Å
AuthorsNielsen, J.A. / Slaaby, R. / Boesen, T. / Hummelshoj, T. / Brandt, J. / Schluckebier, G. / Nissen, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Other government Denmark
CitationJournal: J Mol Biol / Year: 2022
Title: Structural Investigations of Full-Length Insulin Receptor Dynamics and Signalling.
Authors: Jeppe Nielsen / Jakob Brandt / Thomas Boesen / Tina Hummelshøj / Rita Slaaby / Gerd Schluckebier / Poul Nissen /
Abstract: Insulin regulates glucose homeostasis via binding and activation of the insulin receptor dimer at two distinct pairs of binding sites 1 and 2. Here, we present cryo-EM studies of full-length human ...Insulin regulates glucose homeostasis via binding and activation of the insulin receptor dimer at two distinct pairs of binding sites 1 and 2. Here, we present cryo-EM studies of full-length human insulin receptor (hIR) in an active state obtained at non-saturating, physiologically relevant insulin conditions. Insulin binds asymmetrically to the receptor under these conditions, occupying up to three of the four possible binding sites. Deletion analysis of the receptor together with site specific peptides and insulin analogs used in binding studies show that both sites 1 and 2 are required for high insulin affinity. We identify a homotypic interaction of the fibronectin type III domain (FnIII-3) of IR resulting in tight interaction of membrane proximal domains of the active, asymmetric receptor dimer. Our results show how insulin binding at two distinct types of sites disrupts the autoinhibited apo-IR dimer and stabilizes the active dimer. We propose an insulin binding and activation mechanism, which is sequential, exhibits negative cooperativity, and is based on asymmetry at physiological insulin concentrations with one to three insulin molecules activating IR.
History
DepositionAug 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 6, 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

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Structure visualization

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Assembly

Deposited unit
A: Isoform Short of Insulin receptor
B: Isoform Short of Insulin receptor
C: Insulin
D: Insulin
I: Insulin
J: Insulin


Theoretical massNumber of molelcules
Total (without water)325,0306
Polymers325,0306
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11140 Å2
ΔGint-69 kcal/mol
Surface area78020 Å2
MethodPISA

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Components

#1: Protein Isoform Short of Insulin receptor / IR


Mass: 156697.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P06213, receptor protein-tyrosine kinase
#2: Protein/peptide Insulin


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#3: Protein/peptide Insulin


Mass: 3433.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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: DDM solubilised full-length human insulin receptor with three insulins bound
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.46 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
250 mMHepesC8H18N2O4S1
30.03 w/v%DDMC24H46O111
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K / Details: Blotted for 3s prior to plunging

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 15 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
7NAMDmodel fitting
9PHENIX1.19.2model refinementReal-space refinement
13cryoSPARC2.153D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.1 Å / Resolution method: OTHER / Num. of particles: 26701 / Details: Masked FSC calculated with GSFSC in cryoSPARC2. / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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