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- EMDB-24761: Insulin Degrading Enzyme pC/pC -

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Basic information

Entry
Database: EMDB / ID: EMD-24761
TitleInsulin Degrading Enzyme pC/pC
Map dataInsulin Degrading Enzyme pC/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 / 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 / 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 / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade
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
Similarity search - Domain/homology
Insulin / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24761.png

Downloads & links

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Map

FileDownload / File: emd_24761.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInsulin Degrading Enzyme pC/pC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.555 Å		1.08 Å/pix.
x 256 pix.
= 277.555 Å		1.08 Å/pix.
x 256 pix.
= 277.555 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.23674881 - 0.33687672
Average (Standard dev.)-0.000013395743 (±0.008599743)
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: 2 / 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: 2 / 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1341061
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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