8DZV

Chicken anti-cardiac Troponin I antibody in complex with peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design of Polarity-Dependent Immunosensors Based on the Structural Analysis of Engineered Antibodies.

Islam, J.Conroy, P.Fercher, C.Kim, M.Yaari, Z.Jones, M.Bell, T.D.M.Caradoc-Davies, T.Law, R.Whisstock, J.Heller, D.Mahler, S.Corrie, S.

(2023) ACS Chem Biol 18: 1863-1871

  • DOI: https://doi.org/10.1021/acschembio.3c00303
  • Primary Citation of Related Structures:  
    8DZV

  • PubMed Abstract: 

    "Reagentless" immunosensors are emerging to address the challenge of practical and sensitive detection of important biomarkers in real biological samples without the need for multistep assays and user intervention, with applications ranging from research tools to point-of-care diagnostics. Selective target binding to an affinity reagent is detected and reported in one step without the need for washing or additional reporters. In this study, we used a structure-guided approach to identify a mutation site in an antibody fragment for the polarity-dependent fluorophore, Anap, such that upon binding of the protein target cardiac troponin I, the Anap-labeled antibody would produce a detectable and dose-dependent shift in emission wavelength. We observed a significant emission wavelength shift of the Anap-labeled anti-cTnI mutant, with a blue shift of up to 37 nm, upon binding to the cTnI protein. Key differences in the resulting emission spectra between target peptides in comparison to whole proteins were also found; however, the affinity and binding characteristics remained unaffected when compared to the wild-type antibody. We also highlighted the potential flexibility of the approach by incorporating a near-infrared dye, IRDye800CW, into the same mutation site, which also resulted in a dose-dependent wavelength shift upon target incubation. These reagents can be used in experiments and devices to create simpler and more efficient biosensors across a range of research, medical laboratory, and point-of-care platforms.


  • Organizational Affiliation

    Department of Chemical and Biological Engineering, Monash University, Melbourne 3800, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
scfv 2B12277Gallus gallusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cTnI peptideB [auth C]13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P19429 (Homo sapiens)
Explore P19429 
Go to UniProtKB:  P19429
PHAROS:  P19429
GTEx:  ENSG00000129991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19429
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.8α = 90
b = 74.21β = 90
c = 75.43γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary