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- EMDB-24757: Insulin Degrading Enzyme pO/pC -

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Basic information

Entry
Database: EMDB / ID: EMD-24757
TitleInsulin Degrading Enzyme pO/pC
Map dataInsulin Degrading Enzyme pO/pC
Sample
  • Complex: Cysteine-free Insulin-degrading enzyme in complex with Insulin A chain and Insulin B chain
    • Complex: Cysteine-free Insulin-degrading enzyme
      • Protein or peptide: Cysteine-free Insulin-degrading enzyme
    • Complex: Insulin A chain, Insulin B chain
      • Protein or peptide: Insulin A chain
      • Protein or peptide: Insulin B chain
KeywordsM16A zinc metalloprotease / HYDROLASE
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 / 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 / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / peptide catabolic process / Signaling by Insulin receptor / nitric oxide-cGMP-mediated signaling / IRS activation / Insulin processing / regulation of protein secretion / amyloid-beta clearance / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / 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 / positive regulation of nitric oxide mediated signal transduction / fatty acid homeostasis / amyloid-beta metabolic process / regulation of protein localization to plasma membrane / 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 / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / proteolysis involved in protein catabolic process / 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 nitric-oxide synthase activity / positive regulation of cell differentiation / negative regulation of proteolysis / Peroxisomal protein import / regulation of transmembrane transporter activity / peptide binding / wound healing / regulation of synaptic plasticity / protein catabolic process / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / cognition / positive regulation of neuron projection development / Golgi lumen / positive regulation of protein localization to nucleus / peroxisome / positive regulation of protein catabolic process / vasodilation / glucose metabolic process / regulation of protein localization / positive regulation of protein binding / virus receptor activity / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / 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
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / 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 ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Insulin / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMancl JM / Liang WG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To be published
Title: Ensemble cryoEM reveals a substrate-induced shift in the conformational dynamics of human insulin degrading enzyme
Authors: Mancl JM / Liang WG / Wei H / Carragher B / Potter CS / Tang WJ
History
DepositionAug 27, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24757.png

Downloads & links

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Map

FileDownload / File: emd_24757.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInsulin Degrading Enzyme pO/pC
Voxel sizeX=Y=Z: 1.0842 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.12028788 - 0.22222795
Average (Standard dev.)-0.000012501205 (±0.006741864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.5552 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cysteine-free Insulin-degrading enzyme in complex with Insulin A ...

EntireName: Cysteine-free Insulin-degrading enzyme in complex with Insulin A chain and Insulin B chain
Components
  • Complex: Cysteine-free Insulin-degrading enzyme in complex with Insulin A chain and Insulin B chain
    • Complex: Cysteine-free Insulin-degrading enzyme
      • Protein or peptide: Cysteine-free Insulin-degrading enzyme
    • Complex: Insulin A chain, Insulin B chain
      • Protein or peptide: Insulin A chain
      • Protein or peptide: Insulin B chain

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Supramolecule #1: Cysteine-free Insulin-degrading enzyme in complex with Insulin A ...

SupramoleculeName: Cysteine-free Insulin-degrading enzyme in complex with Insulin A chain and Insulin B chain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Cysteine-free Insulin-degrading enzyme

SupramoleculeName: Cysteine-free Insulin-degrading enzyme / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Insulin A chain, Insulin B chain

SupramoleculeName: Insulin A chain, Insulin B chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cysteine-free Insulin-degrading enzyme

MacromoleculeName: Cysteine-free 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: 117.068508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRYRLAWLLH PALPSTFRSV LGARLPPPER LCGFQKKTYS KMNNPAIKRI GNHITKSPED KREYRGLELA NGIKVLLISD PTTDKSSAA LDVHIGSLSD PPNIAGLSHF LEHMLFLGTK KYPKENEYSQ FLSEHAGSSN AFTSGEHTNY YFDVSHEHLE G ALDRFAQF ...String:
MRYRLAWLLH PALPSTFRSV LGARLPPPER LCGFQKKTYS KMNNPAIKRI GNHITKSPED KREYRGLELA NGIKVLLISD PTTDKSSAA LDVHIGSLSD PPNIAGLSHF LEHMLFLGTK KYPKENEYSQ FLSEHAGSSN AFTSGEHTNY YFDVSHEHLE G ALDRFAQF FLSPLFDESA KDREVNAVDS EHEKNVMNDA WRLFQLEKAT GNPKHPFSKF GTGNKYTLET RPNQEGIDVR QE LLKFHSA YYSSNLMAVV VLGRESLDDL TNLVVKLFSE VENKNVPLPE FPEHPFQEEH LKQLYKIVPI KDIRNLYVTF PIP DLQKYY KSNPGHYLGH LIGHEGPGSL LSELKSKGWV NTLVGGQKEG ARGFMFFIIN VDLTEEGLLH VEDIILHMFQ YIQK LRAEG PQEWVFQELK DLNAVAFRFK DKERPRGYTS KIAGILHYYP LEEVLTAEYL LEEFRPDLIE MVLDKLRPEN VRVAI VSKS FEGKTDRTEE WYGTQYKQEA IPDEVIKKWQ NADLNGKFKL PTKNEFIPTN FEILPLEKEA TPYPALIKDT AMSKLW FKQ DDKFFLPKAN LNFEFFSPFA YVDPLHSNMA YLYLELLKDS LNEYAYAAEL AGLSYDLQNT IYGMYLSVKG YNDKQPI LL KKIIEKMATF EIDEKRFEII KEAYMRSLNN FRAEQPHQHA MYYLRLLMTE VAWTKDELKE ALDDVTLPRL KAFIPQLL S RLHIEALLHG NITKQAALGI MQMVEDTLIE HAHTKPLLPS QLVRYREVQL PDRGWFVYQQ RNEVHNNSGI EIYYQTDMQ STSENMFLEL FAQIISEPAF NTLRTKEQLG YIVFSGPRRA NGIQGLRFII QSEKPPHYLE SRVEAFLITM EKSIEDMTEE AFQKHIQAL AIRRLDKPKK LSAESAKYWG EIISQQYNFD RDNTEVAYLK TLTKEDIIKF YKEMLAVDAP RRHKVSVHVL A REMDSSPV VGEFPSQNDI NLSQAPALPQ PEVIQNMTEF KRGLPLFPLV KPH

UniProtKB: Insulin-degrading enzyme

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Macromolecule #2: Insulin A chain

MacromoleculeName: Insulin A chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.383698 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
GIVEQCCTSI CSLYQLENYC N

UniProtKB: Insulin

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Macromolecule #3: Insulin B chain

MacromoleculeName: Insulin B chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.417931 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
FVNQHLCGSH LVEALYLVCG ERGFFYTPLT

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

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Instrument: SPOTITON

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76379

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