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- EMDB-7062: Cryo-EM structure of human insulin degrading enzyme in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-7062
TitleCryo-EM structure of human insulin degrading enzyme in complex with insulin
Map dataInsulin degrading enzyme in complex with insulin
Sample
  • Complex: Insulin degrading enzyme/Insulin
    • Protein or peptide: Insulin-degrading enzyme
    • Protein or peptide: FAB H11-E heavy chain
    • Protein or peptide: FAB H11-E light chain
    • Protein or peptide: Insulin
KeywordsIDE / insulin degrading enzyme / amyloid beta / BIOSYNTHETIC PROTEIN / HYDROLASE-IMMUNE SYSTEM-HORMONE complex
Function / homology
Function and homology information


insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / negative regulation of NAD(P)H oxidase activity / regulation of aerobic respiration ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / negative regulation of NAD(P)H oxidase activity / regulation of aerobic respiration / immunoglobulin complex / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / peptide catabolic process / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / amyloid-beta clearance / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / peroxisomal matrix / positive regulation of protein autophosphorylation / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / amyloid-beta metabolic process / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / peptide binding / proteolysis involved in protein catabolic process / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / Peroxisomal protein import / wound healing / protein catabolic process / negative regulation of protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / metalloendopeptidase activity / positive regulation of protein localization to nucleus / Golgi lumen / cognition / glucose metabolic process / positive regulation of protein catabolic process / positive regulation of protein binding / vasodilation / peroxisome / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / virus receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / positive regulation of cell growth / basolateral plasma membrane / secretory granule lumen / endopeptidase activity / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 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 / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Insulin / Immunoglobulin gamma-1 heavy chain / Insulin-degrading enzyme / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang Z / Liang WG / Bailey LJ / Tan YZ / Wei H / Kossiakoff AA / Carragher B / Potter SC / Tang WJ
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM81539 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121964 United States
Simons Foundation349247 United States
CitationJournal: 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- ...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
DepositionOct 3, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseDec 27, 2017-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.024
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  • Surface view with fitted model
  • Atomic models: PDB-6b70
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7062.png

Downloads & links

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Map

FileDownload / File: emd_7062.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInsulin degrading enzyme in complex with insulin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 343.36 Å		1.07 Å/pix.
x 320 pix.
= 343.36 Å		1.07 Å/pix.
x 320 pix.
= 343.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.073 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.057205748 - 0.14735058
Average (Standard dev.)0.00040003893 (±0.0041737817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 343.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0731.0731.073
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z343.360343.360343.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0570.1470.000

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Supplemental data

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Mask #1

Fileemd_7062_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Insulin degrading enzyme in complex with insulin

Fileemd_7062_half_map_1.map
AnnotationInsulin degrading enzyme in complex with insulin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Insulin degrading enzyme in complex with insulin

Fileemd_7062_half_map_2.map
AnnotationInsulin degrading enzyme in complex with insulin
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Insulin degrading enzyme/Insulin

EntireName: Insulin degrading enzyme/Insulin
Components
  • Complex: Insulin degrading enzyme/Insulin
    • Protein or peptide: Insulin-degrading enzyme
    • Protein or peptide: FAB H11-E heavy chain
    • Protein or peptide: FAB H11-E light chain
    • Protein or peptide: Insulin

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Supramolecule #1: Insulin degrading enzyme/Insulin

SupramoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Insulin-degrading enzyme

MacromoleculeName: Insulin-degrading enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: insulysin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.866484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: FAB H11-E heavy chain

MacromoleculeName: FAB H11-E heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.057748 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFNIS SSSIHWVRQA PGKGLEWVAS IYSYSGSTYY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARH YSAVAGLDYW GQGTLVTVFN QIKPPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFNIS SSSIHWVRQA PGKGLEWVAS IYSYSGSTYY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARH YSAVAGLDYW GQGTLVTVFN QIKPPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP

UniProtKB: Immunoglobulin gamma-1 heavy chain

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Macromolecule #3: FAB H11-E light chain

MacromoleculeName: FAB H11-E light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.087609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD YTLTISSLQP EDFATYYCQ QSYFNPITFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD YTLTISSLQP EDFATYYCQ QSYFNPITFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNR

UniProtKB: Ig-like domain-containing protein

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Macromolecule #4: Insulin

MacromoleculeName: Insulin / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.989862 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALWMRLLPL LALLALWGPD PAAAFVNQHL CGSHLVEALY LVCGERGFFY TPKTRREAED LQVGQVELGG GPGAGSLQPL ALEGSLQKR GIVEQCCTSI CSLYQLENYC N

UniProtKB: Insulin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mmol/LC8H18N2O4SHEPES
300.0 mmol/LNaClSodium chloride
20.0 mmol/LC10H16N2O8EDTA
GridModel: Homemade / Material: COPPER / 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
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER
Details: The cryo grids were made using Spotiton and homemade plunger.
DetailsThe sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Alignment procedureComa free - Residual tilt: 10.0 mrad
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen 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

Particle selectionNumber selected: 762283
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3qz2

Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 116122
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 2
Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 2
Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 8 / Avg.num./class: 18549 / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 92
Output model

PDB-6b70:
Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy chain, FAB H11-E light chain and insulin

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