5CJO | pdb_00005cjo

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 
    0.245 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5CJO

This is version 1.5 of the entry. See complete history

Literature

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.

Bailey, L.J.Sheehy, K.M.Dominik, P.K.Liang, W.G.Rui, H.Clark, M.Jaskolowski, M.Kim, Y.Deneka, D.Tang, W.J.Kossiakoff, A.A.

(2017) J Mol Biology 

  • DOI: https://doi.org/10.1016/j.jmb.2017.12.012
  • Primary Citation Related Structures: 
    5CJO, 6AYZ, 6AZ2

  • PubMed Abstract: 

    Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.

Macromolecule Content 

  • Total Structure Weight: 166.31 kDa 
  • Atom Count: 10,966 
  • Modeled Residue Count: 1,371 
  • Deposited Residue Count: 1,465 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin-degrading enzyme990Homo 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
GTEx:  ENSG00000119912 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14735
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB Heavy chain with engineered elbowB [auth H]239Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB light chainC [auth L]216Mus musculusMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
InsulinD [auth a]20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
GTEx:  ENSG00000254647 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
E [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free:  0.245 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.689α = 90
b = 109.218β = 90
c = 263.405γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

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 StatesGM117372
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM087519
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094588

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-01-10
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary