2WC0

crystal structure of human insulin degrading enzyme in complex with iodinated insulin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Molecular Basis of Catalytic Chamber-Assisted Unfolding and Cleavage of Human Insulin by Human Insulin Degrading Enzyme.

Manolopoulou, M., Guo, Q., Malito, E., Schilling, A.B., Tang, W.J.

(2009) J Biol Chem 284: 14177

  • DOI: 10.1074/jbc.M900068200
  • Primary Citation of Related Structures:  
    2WBY, 2WC0

  • PubMed Abstract: 

    • Insulin is a hormone vital for glucose homeostasis, and insulin-degrading enzyme (IDE) plays a key role in its clearance. IDE exhibits a remarkable specificity to degrade insulin without breaking the disulfide bonds that hold the insulin A and B chains together ...

    Insulin is a hormone vital for glucose homeostasis, and insulin-degrading enzyme (IDE) plays a key role in its clearance. IDE exhibits a remarkable specificity to degrade insulin without breaking the disulfide bonds that hold the insulin A and B chains together. Using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to obtain high mass accuracy, and electron capture dissociation (ECD) to selectively break the disulfide bonds in gas phase fragmentation, we determined the cleavage sites and composition of human insulin fragments generated by human IDE. Our time-dependent analysis of IDE-digested insulin fragments reveals that IDE is highly processive in its initial cleavage at the middle of both the insulin A and B chains. This ensures that IDE effectively splits insulin into inactive N- and C-terminal halves without breaking the disulfide bonds. To understand the molecular basis of the recognition and unfolding of insulin by IDE, we determined a 2.6-A resolution insulin-bound IDE structure. Our structure reveals that IDE forms an enclosed catalytic chamber that completely engulfs and intimately interacts with a partially unfolded insulin molecule. This structure also highlights how the unique size, shape, charge distribution, and exosite of the IDE catalytic chamber contribute to its high affinity ( approximately 100 nm) for insulin. In addition, this structure shows how IDE utilizes the interaction of its exosite with the N terminus of the insulin A chain as well as other properties of the catalytic chamber to guide the unfolding of insulin and allowing for the processive cleavages.

    Organizational Affiliation: 

    Ben-May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INSULIN-DEGRADING ENZYME A, B990Homo sapiensMutation(s): 14 
Gene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Explore P14735 
Go to UniProtKB:  P14735
NIH Common Fund Data Resources
PHAROS:  P14735
GTEx:  ENSG00000119912
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
INSULIN A CHAIN C, E21Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
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PHAROS:  P01308
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
INSULIN B CHAIN D, F30Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS:  P01308
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 263.169α = 90
b = 263.169β = 90
c = 90.875γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance