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- EMDB-7041: Cryo-EM structure of human insulin degrading enzyme in complex wi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7041 | |||||||||||||||
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Title | Cryo-EM structure of human insulin degrading enzyme in complex with insulin | |||||||||||||||
![]() | This is the sharpened map from the final, Insulin degrading enzyme in complex with insulin | |||||||||||||||
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Function / homology | ![]() insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / ubiquitin-modified protein reader activity / insulin binding / negative regulation of NAD(P)H oxidase activity ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / ubiquitin-modified protein reader activity / insulin binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / regulation of aerobic respiration / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / peptide catabolic process / Insulin processing / regulation of protein secretion / amyloid-beta clearance / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / peroxisomal matrix / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / amyloid-beta metabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / proteolysis involved in protein catabolic process / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / Regulation of insulin secretion / acute-phase response / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of cell differentiation / Peroxisomal protein import / negative regulation of proteolysis / regulation of transmembrane transporter activity / peptide binding / insulin-like growth factor receptor binding / wound healing / protein catabolic process / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / cognition / metalloendopeptidase activity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / positive regulation of protein catabolic process / vasodilation / peroxisome / glucose metabolic process / regulation of protein localization / positive regulation of protein binding / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / basolateral plasma membrane / secretory granule lumen Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
![]() | Zhang Z / Liang WG / Bailey LJ / Tan YZ / Wei H / Kossiakoff AA / Carragher B / Potter SC / Tang WJ | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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- ...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. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.9 KB 26.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 56.3 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() ![]() | 97.6 MB 98.4 MB 98.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 552.6 KB | Display | ![]() |
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Full document | ![]() | 552.2 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b3qMC ![]() 6bfcMC ![]() 7062C ![]() 7065C ![]() 7066C ![]() 7090C ![]() 7091C ![]() 7092C ![]() 7093C ![]() 5wobC ![]() 6b70C ![]() 6b7yC ![]() 6b7zC ![]() 6bf6C ![]() 6bf7C ![]() 6bf8C ![]() 6bf9C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | This is the sharpened map from the final, Insulin degrading enzyme in complex with insulin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: This is the full, unfiltered map from final...
File | emd_7041_additional.map | ||||||||||||
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Annotation | This is the full, unfiltered map from final refinement for insulin degrading enzyme in complex with insulin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: This is the first half map from the...
File | emd_7041_half_map_1.map | ||||||||||||
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Annotation | This is the first half map from the final refinement for insulin degrading enzyme in complex with insulin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: This is the second half map from the...
File | emd_7041_half_map_2.map | ||||||||||||
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Annotation | This is the second half map from the final refinement for insulin degrading enzyme in complex with insulin | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Insulin degrading enzyme/Insulin
Entire | Name: Insulin degrading enzyme/Insulin |
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Components |
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-Supramolecule #1: Insulin degrading enzyme/Insulin
Supramolecule | Name: Insulin degrading enzyme/Insulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Cryo-EM structure of human insulin degrading enzyme in complex with insulin |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Experimental: 100 KDa |
-Macromolecule #1: Insulin-degrading enzyme
Macromolecule | Name: Insulin-degrading enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: insulysin |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 114.561562 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHAAG IPMNNPAIKR IGNHITKSPE DKREYRGLEL ANGIKVLLIS DPTTDKSSAA LDVHIGSLSD PPNIAGLSHF LEHMLFLGT KKYPKENEYS QFLSEHAGSS NAFTSGEHTN YYFDVSHEHL EGALDRFAQF FLSPLFDESA KDREVNAVDS E HEKNVMND ...String: MHHHHHHAAG IPMNNPAIKR IGNHITKSPE DKREYRGLEL ANGIKVLLIS DPTTDKSSAA LDVHIGSLSD PPNIAGLSHF LEHMLFLGT KKYPKENEYS QFLSEHAGSS NAFTSGEHTN YYFDVSHEHL EGALDRFAQF FLSPLFDESA KDREVNAVDS E HEKNVMND AWRLFQLEKA TGNPKHPFSK FGTGNKYTLE TRPNQEGIDV RQELLKFHSA YYSSNLMAVV VLGRESLDDL TN LVVKLFS EVENKNVPLP EFPEHPFQEE HLKQLYKIVP IKDIRNLYVT FPIPDLQKYY KSNPGHYLGH LIGHEGPGSL LSE LKSKGW VNTLVGGQKE GARGFMFFII NVDLTEEGLL HVEDIILHMF QYIQKLRAEG PQEWVFQELK DLNAVAFRFK DKER PRGYT SKIAGILHYY PLEEVLTAEY LLEEFRPDLI EMVLDKLRPE NVRVAIVSKS FEGKTDRTEE WYGTQYKQEA IPDEV IKKW QNADLNGKFK LPTKNEFIPT NFEILPLEKE ATPYPALIKD TAMSKLWFKQ DDKFFLPKAN LNFEFFSPFA YVDPLH SNM AYLYLELLKD SLNEYAYAAE LAGLSYDLQN TIYGMYLSVK GYNDKQPILL KKIIEKMATF EIDEKRFEII KEAYMRS LN NFRAEQPHQH AMYYLRLLMT EVAWTKDELK EALDDVTLPR LKAFIPQLLS RLHIEALLHG NITKQAALGI MQMVEDTL I EHAHTKPLLP SQLVRYREVQ LPDRGWFVYQ QRNEVHNNSG IEIYYQTDMQ STSENMFLEL FAQIISEPAF NTLRTKEQL GYIVFSGPRR ANGIQGLRFI IQSEKPPHYL ESRVEAFLIT MEKSIEDMTE EAFQKHIQAL AIRRLDKPKK LSAESAKYWG EIISQQYNF DRDNTEVAYL KTLTKEDIIK FYKEMLAVDA PRRHKVSVHV LAREMDSNPV VGEFPAQNDI NLSQAPALPQ P EVIQNMTE FKRGLPLFPL VKPHINFMAA KL |
-Macromolecule #2: Insulin
Macromolecule | Name: Insulin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.989862 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MALWMRLLPL LALLALWGPD PAAAFVNQHL CGSHLVEALY LVCGERGFFY TPKTRREAED LQVGQVELGG GPGAGSLQPL ALEGSLQKR GIVEQCCTSI CSLYQLENYC N |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: homemade nanowire grid / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.001 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER Details: The cryo grids were made using Spotiton and homemade plunger. | ||||||||||||
Details | The sample was monodisperse |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Alignment procedure | Coma free - Residual tilt: 10.0 mrad |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-50 / Number grids imaged: 3 / Number real images: 3085 / Average exposure time: 10.0 sec. / Average electron dose: 71.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 46598 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9400000000000001 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |