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 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.7554/eLife.33572
  • Primary Citation of Related Structures:  
    5WOB, 6B3Q, 6B70, 6B7Y, 6B7Z, 6BF6, 6BF7, 6BF8, 6BF9, 6BFC

  • 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 remained unsolved ...

    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: 

    Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin-degrading enzyme
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
990Homo sapiensMutation(s): 14 
Gene Names: IDE
EC: 3.4.24.56
UniProt & NIH Common Fund Data Resources
Find proteins for P14735 (Homo sapiens)
Explore P14735 
Go to UniProtKB:  P14735
PHAROS:  P14735
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UniProt GroupP14735
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin20Homo sapiensMutation(s): 0 
Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
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UniProt GroupP01308
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
IDE-bound Fab heavy chain263Mus musculoidesMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
IDE-bound Fab light chain239Mus musculoidesMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.589α = 90
b = 138.19β = 99.36
c = 376.509γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM121964

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2022-03-23
    Changes: Author supporting evidence, Database references