5WOB

Crystal Structure Analysis of Fab1-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Insulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme.

Zhang, Z.Liang, W.G.Bailey, L.J.Tan, Y.Z.Wei, H.Wang, A.Farcasanu, M.Woods, V.A.McCord, L.A.Lee, D.Shang, W.Deprez-Poulain, R.Deprez, B.Liu, D.R.Koide, A.Koide, S.Kossiakoff, A.A.Li, S.Carragher, B.Potter, C.S.Tang, W.J.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.33572
  • Primary Citation of Related Structures:  

  • PubMed 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 peptides that tend to form amyloid fibrils remaine ...

    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.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,New York University Langone Medical Center, New York University School of Medicine, New York, United States.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States.,Department of Medicine, University of California, San Diego, La Jolla, United States.,Univ. Lille, INSERM, Institut Pasteur de Lille, Lille, France.,Perlmutter Cancer Center, New York University School of Medicine, New York, United States.,BioCAT, Argonne National Laboratory, Illinois, United States.,National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.,Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin-degrading enzyme
A, B, C, D, E, F, G, H
990Homo sapiensMutation(s): 14 
Gene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Go to Gene View: IDE
Go to UniProtKB:  P14735
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Insulin
a, b, c, d, e, f, g, h
20Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
IDE-bound Fab heavy chain
I, K, M, O, Q, S, U, W
263N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
IDE-bound Fab light chain
J, L, N, P, R, T, V, X
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 121.589α = 90.00
b = 138.190β = 99.36
c = 376.509γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2019-10-30
    Type: Data collection, Database references