8RTX | pdb_00008rtx

Crystal Structure of an Anti-idiotype Fab Fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.269 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural insights into ternary immunocomplex formation and cross-reactivity: binding of an anti-immunocomplex FabB12 to Fab220-testosterone complex.

Eronen, V.Takkinen, K.Torni, A.Peng, K.Janis, J.Parkkinen, T.Hakulinen, N.Rouvinen, J.

(2024) FEBS J 291: 4744-4756

  • DOI: https://doi.org/10.1111/febs.17258
  • Primary Citation Related Structures: 
    8RTW, 8RTX

  • PubMed Abstract: 

    Anti-immunocomplex (Anti-IC) antibodies have been used in developing noncompetitive immunoassays for detecting small molecule analytics (haptens). These antibodies bind specifically to the primary antibody in complex with hapten. Although several anti-IC antibody-based immunoassays have been developed, structural studies of these systems are very limited. In this study, we determined the crystal structures of anti-testosterone Fab220 in complex with testosterone and the corresponding anti-IC antibody FabB12. The structure of the ternary complex of testosterone, Fab220, and FabB12 was predicted using LightDock and AlphaFold. The ternary complex has a large (~ 1100 Å 2 ) interface between antibodies. The A-ring of the testosterone bound by Fab220 also participates in the binding of the anti-IC antibody. The structural analysis was complemented by native mass spectrometry. The affinities for testosterone (TES) and three cross-reactive steroids [dihydrotestosterone (DHT), androstenedione (A4), and dehydroepiandrosterone sulfate (DHEA-S)] were measured, and ternary complex formation was studied. The results clearly show the ternary complex formation in the solution. Although DHT showed significant cross-reactivity, A4 and DHEA-S exhibited minor cross-reactivity.


  • Organizational Affiliation
    • Department of Chemistry, University of Eastern Finland, Joensuu, Finland.

Macromolecule Content 

  • Total Structure Weight: 141.14 kDa 
  • Atom Count: 9,738 
  • Modeled Residue Count: 1,305 
  • Deposited Residue Count: 1,323 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-IC Fab fragment B12 light chain
A, C, E
214Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-IC Fab fragment B12 heavy chain
B, D, F
227Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.269 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.857α = 90
b = 81.857β = 90
c = 181.927γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2024-11-13
    Changes: Database references