[English] 日本語
Yorodumi
- PDB-6bfc: Cryo-EM structure of human insulin degrading enzyme in complex wi... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6bfc
TitleCryo-EM structure of human insulin degrading enzyme in complex with insulin
Components
  • Insulin-degrading enzyme
  • Insulin
KeywordsHYDROLASE/HORMONE / IDE / amyloid beta / HORMONE / HYDROLASE-HORMONE complex
Function/homologyinsulysin / beta-endorphin binding / Peptidase M16, middle/third domain / bradykinin catabolic process / insulin catabolic process / ubiquitin recycling / insulin metabolic process / ubiquitin-dependent protein binding / hormone catabolic process / Middle or third domain of peptidase_M16 ...insulysin / beta-endorphin binding / Peptidase M16, middle/third domain / bradykinin catabolic process / insulin catabolic process / ubiquitin recycling / insulin metabolic process / ubiquitin-dependent protein binding / hormone catabolic process / Middle or third domain of peptidase_M16 / Insulinase family, zinc-binding region signature. / Peptidase M16, zinc-binding site / Peptidase M16, N-terminal / Peptidase M16, C-terminal / cytosolic proteasome complex / Metalloenzyme, LuxS/M16 peptidase-like / insulin binding / peroxisomal matrix / amyloid-beta clearance / negative regulation of glycogen catabolic process / alpha-beta T cell activation / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / negative regulation of NAD(P)H oxidase activity / negative regulation of protein oligomerization / regulation of transmembrane transporter activity / Insulin receptor recycling / Signaling by Insulin receptor / negative regulation of respiratory burst involved in inflammatory response / IRS activation / Insulin processing / positive regulation of respiratory burst / determination of adult lifespan / positive regulation of dendritic spine maintenance / regulation of protein secretion / Insulin / Regulation of gene expression in beta cells / negative regulation of protein secretion / Peptidase M16 inactive domain / Regulation of insulin secretion / positive regulation of protein oligomerization / Insulinase (Peptidase family M16) / positive regulation of peptide hormone secretion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of lipid biosynthetic process / Insulin family / negative regulation of blood vessel diameter / negative regulation of reactive oxygen species biosynthetic process / Insulin-like / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / fatty acid homeostasis / Insulin/IGF/Relaxin family / Synthesis, secretion, and deacylation of Ghrelin / regulation of cellular amino acid metabolic process / cognition / positive regulation of glycolytic process / positive regulation of cellular protein metabolic process / COPI-mediated anterograde transport / positive regulation of glycogen biosynthetic process / Signal attenuation / positive regulation of insulin receptor signaling pathway / go:0015758: / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / regulation of protein localization to plasma membrane / regulation of synaptic plasticity / endosome lumen / positive regulation of brown fat cell differentiation / negative regulation of acute inflammatory response / positive regulation of cytokine secretion / proteolysis involved in cellular protein catabolic process / positive regulation of protein autophosphorylation / Insulin receptor signalling cascade / insulin-like growth factor receptor binding / positive regulation of mitotic nuclear division / amyloid-beta metabolic process / regulation of protein localization / positive regulation of cell differentiation / positive regulation of protein catabolic process / positive regulation of long-term synaptic potentiation / peptide binding / positive regulation of glucose import / activation of protein kinase B activity / negative regulation of protein catabolic process / negative regulation of proteolysis / positive regulation of nitric-oxide synthase activity / insulin receptor signaling pathway / protein heterooligomerization / acute-phase response / insulin receptor binding / hormone activity / peroxisome / positive regulation of DNA replication / positive regulation of protein localization to nucleus / positive regulation of blood vessel diameter
Function and homology information
Specimen sourceHomo sapiens / / human
MethodElectron microscopy (3.7 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsLiang, W.G. / Zhang, Z. / Bailey, L.J. / Kossiakoff, A.A. / Tan, Y.Z. / Wei, H. / Carragher, B. / Potter, S.C. / Tang, W.J.
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-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.
Copyright: 2018, Zhang et al.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 26, 2017 / Release: Dec 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 27, 2017Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.2Apr 11, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

Downloads & links

-
Assembly

Deposited unit
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
a: Insulin
b: Insulin


Theoretical massNumber of molelcules
Total (without water)247,7134
Polyers247,7134
Non-polymers00
Water0
1
A: Insulin-degrading enzyme
a: Insulin


Theoretical massNumber of molelcules
Total (without water)123,8562
Polyers123,8562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
B: Insulin-degrading enzyme
b: Insulin


Theoretical massNumber of molelcules
Total (without water)123,8562
Polyers123,8562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein/peptide Insulin-degrading enzyme / / Abeta-degrading protease / Insulin protease / Insulinase / Insulysin


Mass: 111866.484 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / / human / Gene: IDE / Production host: Escherichia coli / Strain (production host): BL21(DE3) / References: UniProt:P14735, EC:3.4.24.56 (insulysin)
#2: Protein/peptide Insulin /


Mass: 11989.862 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / / human / Gene: INS / Production host: Escherichia coli / Strain (production host): BL21(DE3) / References: UniProt:P01308

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: Insulin bound insulin degrading enzyme / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.1 deg. / Units: MEGADALTONS / Experimental value: YES
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Escherichia coli / Strain: BL21(DE3)
Buffer solutionpH: 7.8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
120mmol/lHEPEsC8H18N2O4S1
2300mmol/lSodium ChlorideNaCl1
320mmol/lEDTAC10H16N2O81
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Homemade
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 293 kelvins / Details: Grids made using Spotiton

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 / Calibrated magnification: 46598 / Nominal defocus max: 2200 nm / Nominal defocus min: 940 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 kelvins / Temperature (min): 70 kelvins / Residual tilt: 10 mradians
Image recordingAverage exposure time: 10 sec. / Electron dose: 71.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 3 / Number of real images: 3085
Image scansSampling size: 5 microns / Dimension width: 3710 / Dimension height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1DoG PickerPARTICLE SELECTION
2Leginon3.3IMAGE ACQUISITION
4GctfGctf_v0.50_sm_30_cu7.5X86_64CTF CORRECTION
7Coot0.89_PreMODEL FITTING
8UCSF Chimera1.11.2MODEL FITTING
10RELION2.0INITIAL EULER ASSIGNMENT
12RELION2.0CLASSIFICATION
13RELION2.1RECONSTRUCTION
14PHENIX1.02-2829MODEL REFINEMENT
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 762283
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 148392 / Algorithm: FOURIER SPACE / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingOverall b value: 111.9 / Ref protocol: FLEXIBLE FIT / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616160
ELECTRON MICROSCOPYf_angle_d1.04921857
ELECTRON MICROSCOPYf_dihedral_angle_d9.0169765
ELECTRON MICROSCOPYf_chiral_restr0.0592362
ELECTRON MICROSCOPYf_plane_restr0.0082822

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more