+Open data
-Basic information
Entry | Database: PDB / ID: 7rzi | ||||||
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Title | Insulin Degrading Enzyme pC/pC | ||||||
Components |
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Keywords | HYDROLASE / M16A zinc metalloprotease | ||||||
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 / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / peptide catabolic process / IRS activation / 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 / negative regulation of acute inflammatory response / peroxisomal matrix / 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 / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / 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 / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / Peroxisomal protein import / 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 | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Mancl, J.M. / Liang, W.G. / Tang, W.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Ensemble cryoEM reveals a substrate-induced shift in the conformational dynamics of human insulin degrading enzyme Authors: Mancl, J.M. / Liang, W.G. / Wei, H. / Carragher, B. / Potter, C.S. / Tang, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rzi.cif.gz | 341.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rzi.ent.gz | 279.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rzi_validation.pdf.gz | 824.3 KB | Display | wwPDB validaton report |
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Full document | 7rzi_full_validation.pdf.gz | 849.7 KB | Display | |
Data in XML | 7rzi_validation.xml.gz | 55 KB | Display | |
Data in CIF | 7rzi_validation.cif.gz | 81.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/7rzi ftp://data.pdbj.org/pub/pdb/validation_reports/rz/7rzi | HTTPS FTP |
-Related structure data
Related structure data | 24761MC 7rzeC 7rzfC 7rzgC 7rzhC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 117068.508 Da / Num. of mol.: 2 Mutation: C110L, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966S, C974S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDE / Production host: Escherichia coli (E. coli) / References: UniProt: P14735, insulysin #2: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 #3: Protein/peptide | Mass: 3417.931 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: SPOTITON / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1341061 / Symmetry type: POINT |