|Entry||Database: PDB / ID: 6bfc|
|Title||Cryo-EM structure of human insulin degrading enzyme in complex with insulin|
|Keywords||HYDROLASE/HORMONE / IDE / amyloid beta / HORMONE / HYDROLASE-HORMONE complex|
|Function/homology||insulysin / beta-endorphin binding / Peptidase M16, middle/third domain / bradykinin catabolic process / insulin catabolic process / ubiquitin recycling / insulin metabolic process / ubiquitin-dependent protein binding / hormone catabolic process / Middle or third domain of peptidase_M16 ...insulysin / beta-endorphin binding / Peptidase M16, middle/third domain / bradykinin catabolic process / insulin catabolic process / ubiquitin recycling / insulin metabolic process / ubiquitin-dependent protein binding / hormone catabolic process / Middle or third domain of peptidase_M16 / Insulinase family, zinc-binding region signature. / Peptidase M16, zinc-binding site / Peptidase M16, N-terminal / Peptidase M16, C-terminal / cytosolic proteasome complex / Metalloenzyme, LuxS/M16 peptidase-like / insulin binding / peroxisomal matrix / amyloid-beta clearance / negative regulation of glycogen catabolic process / alpha-beta T cell activation / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / negative regulation of NAD(P)H oxidase activity / negative regulation of protein oligomerization / regulation of transmembrane transporter activity / Insulin receptor recycling / Signaling by Insulin receptor / negative regulation of respiratory burst involved in inflammatory response / IRS activation / Insulin processing / positive regulation of respiratory burst / determination of adult lifespan / positive regulation of dendritic spine maintenance / regulation of protein secretion / Insulin / Regulation of gene expression in beta cells / negative regulation of protein secretion / Peptidase M16 inactive domain / Regulation of insulin secretion / positive regulation of protein oligomerization / Insulinase (Peptidase family M16) / positive regulation of peptide hormone secretion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of lipid biosynthetic process / Insulin family / negative regulation of blood vessel diameter / negative regulation of reactive oxygen species biosynthetic process / Insulin-like / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / fatty acid homeostasis / Insulin/IGF/Relaxin family / Synthesis, secretion, and deacylation of Ghrelin / regulation of cellular amino acid metabolic process / cognition / positive regulation of glycolytic process / positive regulation of cellular protein metabolic process / COPI-mediated anterograde transport / positive regulation of glycogen biosynthetic process / Signal attenuation / positive regulation of insulin receptor signaling pathway / go:0015758: / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / regulation of protein localization to plasma membrane / regulation of synaptic plasticity / endosome lumen / positive regulation of brown fat cell differentiation / negative regulation of acute inflammatory response / positive regulation of cytokine secretion / proteolysis involved in cellular protein catabolic process / positive regulation of protein autophosphorylation / Insulin receptor signalling cascade / insulin-like growth factor receptor binding / positive regulation of mitotic nuclear division / amyloid-beta metabolic process / regulation of protein localization / positive regulation of cell differentiation / positive regulation of protein catabolic process / positive regulation of long-term synaptic potentiation / peptide binding / positive regulation of glucose import / activation of protein kinase B activity / negative regulation of protein catabolic process / negative regulation of proteolysis / positive regulation of nitric-oxide synthase activity / insulin receptor signaling pathway / protein heterooligomerization / acute-phase response / insulin receptor binding / hormone activity / peroxisome / positive regulation of DNA replication / positive regulation of protein localization to nucleus / positive regulation of blood vessel diameter|
Function and homology information
|Specimen source||Homo sapiens / / human|
|Method||Electron microscopy (3.7 Å resolution / Particle / Single particle) / Transmission electron microscopy|
|Authors||Liang, W.G. / Zhang, Z. / Bailey, L.J. / Kossiakoff, A.A. / Tan, Y.Z. / Wei, H. / Carragher, B. / Potter, S.C. / Tang, W.J.|
|Citation||Journal: Elife / Year: 2018|
Title: Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme.
Authors: Zhening Zhang / Wenguang G Liang / Lucas J Bailey / Yong Zi Tan / Hui Wei / Andrew Wang / Mara Farcasanu / Virgil A Woods / Lauren A McCord / David Lee / Weifeng Shang / Rebecca Deprez-Poulain / Benoit Deprez / David R Liu / Akiko Koide / Shohei Koide / Anthony A Kossiakoff / Sheng Li / Bridget Carragher / Clinton S Potter / Wei-Jen Tang
Abstract: Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes ...Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes peptides that tend to form amyloid fibrils remained unsolved. We used cryoEM to understand both the apo- and insulin-bound dimeric IDE states, revealing that IDE displays a large opening between the homologous ~55 kDa N- and C-terminal halves to allow selective substrate capture based on size and charge complementarity. We also used cryoEM, X-ray crystallography, SAXS, and HDX-MS to elucidate the molecular basis of how amyloidogenic peptides stabilize the disordered IDE catalytic cleft, thereby inducing selective degradation by substrate-assisted catalysis. Furthermore, our insulin-bound IDE structures explain how IDE processively degrades insulin by stochastically cutting either chain without breaking disulfide bonds. Together, our studies provide a mechanism for how IDE selectively degrades amyloidogenic peptides and offers structural insights for developing IDE-based therapies.
Copyright: 2018, Zhang et al.
SummaryFull reportAbout validation report
|Date||Deposition: Oct 26, 2017 / Release: Dec 27, 2017|
Downloads & links
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
Mass: 111866.484 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / / human / Gene: IDE / Production host: Escherichia coli / Strain (production host): BL21(DE3) / References: UniProt:P14735, EC:18.104.22.168 (insulysin)
Mass: 11989.862 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / / human / Gene: INS / Production host: Escherichia coli / Strain (production host): BL21(DE3) / References: UniProt:P01308
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Insulin bound insulin degrading enzyme / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Value: 0.1 deg. / Units: MEGADALTONS / Experimental value: YES|
|Source (natural)||Organism: Homo sapiens|
|Source (recombinant)||Organism: Escherichia coli / Strain: BL21(DE3)|
|Buffer solution||pH: 7.8|
|Specimen||Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 / Grid type: Homemade|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 293 kelvins / Details: Grids made using Spotiton|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 22500 / Calibrated magnification: 46598 / Nominal defocus max: 2200 nm / Nominal defocus min: 940 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 kelvins / Temperature (min): 70 kelvins / Residual tilt: 10 mradians|
|Image recording||Average exposure time: 10 sec. / Electron dose: 71.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 3 / Number of real images: 3085|
|Image scans||Sampling size: 5 microns / Dimension width: 3710 / Dimension height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50|
|Software||Name: PHENIX / Version: 1.12_2829: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 762283|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 148392 / Algorithm: FOURIER SPACE / Number of class averages: 2 / Symmetry type: POINT|
|Atomic model building||Overall b value: 111.9 / Ref protocol: FLEXIBLE FIT / Ref space: REAL|
|Refine LS restraints|
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