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- EMDB-7092: 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-7092 | |||||||||||||||
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Title | Cryo-EM structure of human insulin degrading enzyme in complex with insulin | |||||||||||||||
![]() | Insulin degrading enzyme in complex with insulin | |||||||||||||||
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![]() | IDE / insulin degrading enzyme / amyloid beta / BIOSYNTHETIC PROTEIN | |||||||||||||||
Function / homology | ![]() insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / regulation of aerobic respiration / peptide catabolic process ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / Insulin receptor recycling / proteolysis involved in protein catabolic process / Peroxisomal protein import / peptide binding / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / positive regulation of protein catabolic process / positive regulation of protein binding / insulin receptor signaling pathway / peroxisome / virus receptor activity / basolateral plasma membrane / endopeptidase activity / Ub-specific processing proteases / external side of plasma membrane / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.2 KB 24.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 39.8 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() | 98.4 MB 98.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bf8MC ![]() 7041C ![]() 7062C ![]() 7065C ![]() 7066C ![]() 7090C ![]() 7091C ![]() 7093C ![]() 5wobC ![]() 6b3qC ![]() 6b70C ![]() 6b7yC ![]() 6b7zC ![]() 6bf6C ![]() 6bf7C ![]() 6bf9C ![]() 6bfcC 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 | 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 |
-Half map: Insulin degrading enzyme in complex with insulin
File | emd_7092_half_map_1.map | ||||||||||||
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Annotation | Insulin degrading enzyme in complex with insulin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Insulin degrading enzyme in complex with insulin
File | emd_7092_half_map_2.map | ||||||||||||
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Annotation | 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
Entire | Name: Insulin degrading enzyme |
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Components |
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-Supramolecule #1: Insulin degrading enzyme
Supramolecule | Name: Insulin degrading enzyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Cryo-EM structure of human Apo insulin degrading enzyme |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 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: 111.866484 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AIKRIGNHIT KSPEDKREYR GLELANGIKV LLISDPTTDK SSAALDVHIG SLSDPPNIAG LSHFLEHMLF LGTKKYPKEN EYSQFLSEH AGSSNAFTSG EHTNYYFDVS HEHLEGALDR FAQFFLSPLF DESAKDREVN AVDSEHEKNV MNDAWRLFQL E KATGNPKH ...String: AIKRIGNHIT KSPEDKREYR GLELANGIKV LLISDPTTDK SSAALDVHIG SLSDPPNIAG LSHFLEHMLF LGTKKYPKEN EYSQFLSEH AGSSNAFTSG EHTNYYFDVS HEHLEGALDR FAQFFLSPLF DESAKDREVN AVDSEHEKNV MNDAWRLFQL E KATGNPKH PFSKFGTGNK YTLETRPNQE GIDVRQELLK FHSAYYSSNL MAVVVLGRES LDDLTNLVVK LFSEVENKNV PL PEFPEHP FQEEHLKQLY KIVPIKDIRN LYVTFPIPDL QKYYKSNPGH YLGHLIGHEG PGSLLSELKS KGWVNTLVGG QKE GARGFM FFIINVDLTE EGLLHVEDII LHMFQYIQKL RAEGPQEWVF QELKDLNAVA FRFKDKERPR GYTSKIAGIL HYYP LEEVL TAEYLLEEFR PDLIEMVLDK LRPENVRVAI VSKSFEGKTD RTEEWYGTQY KQEAIPDEVI KKWQNADLNG KFKLP TKNE FIPTNFEILP LEKEATPYPA LIKDTAMSKL WFKQDDKFFL PKANLNFEFF SPFAYVDPLH SNMAYLYLEL LKDSLN EYA YAAELAGLSY DLQNTIYGMY LSVKGYNDKQ PILLKKIIEK MATFEIDEKR FEIIKEAYMR SLNNFRAEQP HQHAMYY LR LLMTEVAWTK DELKEALDDV TLPRLKAFIP QLLSRLHIEA LLHGNITKQA ALGIMQMVED TLIEHAHTKP LLPSQLVR Y REVQLPDRGW FVYQQRNEVH NNSGIEIYYQ TDMQSTSENM FLELFAQIIS EPAFNTLRTK EQLGYIVFSG PRRANGIQG LRFIIQSEKP PHYLESRVEA FLITMEKSIE DMTEEAFQKH IQALAIRRLD KPKKLSAESA KYWGEIISQQ YNFDRDNTEV AYLKTLTKE DIIKFYKEML AVDAPRRHKV SVHVLAREMD SCPVVGEFPC QNDINLSQAP ALPQPEVIQN MTEFKRGLPL F PLVKPH UniProtKB: Insulin-degrading enzyme |
-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 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.001 kPa / Details: The grids are homemade lacey gold nanowire grids | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER / Details: The cryo grids were made using Spotiton. | ||||||||||||
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 |
Details | The image was collected at 20-50 degree tilt |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number grids imaged: 1 / #0 - Number real images: 509 / #0 - Average exposure time: 10.0 sec. / #0 - Average electron dose: 7.9 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Digitization - Dimensions - Width: 3710 pixel / #1 - Digitization - Dimensions - Height: 3820 pixel / #1 - Digitization - Frames/image: 1-50 / #1 - Number grids imaged: 1 / #1 - Number real images: 620 / #1 - Average exposure time: 10.0 sec. / #1 - Average electron dose: 6.8 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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 92 |
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Output model | ![]() PDB-6bf8: |