3E8U: Crystal Structure And Thermodynamic Analysis Of Diagnostic Fab 106.3 Complexed With Bnp 5-13 (c10a) Reveal Basis Of Selective Molecular Recognition

B-type natriuretic peptide (BNP) is a naturally secreted regulatory hormone that influences blood pressure and vascular water retention in human physiology. The plasma BNP concentration is a clinically recognized biomarker for various cardiovascular diseases. Quantitative detection of BNP can be achieved in immunoassays using the high-affinity monoclonal IgG1 antibody 106.3, which binds an epitope spanning residues 5-13 of the mature bioactive peptide. To understand the structural basis of this molecular recognition, we crystallized the Fab fragment complexed with the peptide epitope and determined the three-dimensional structure by X-ray diffraction to 2.1 A resolution. The structure reveals the detailed interactions that five of the complementarity-determining regions make with the partially folded peptide. Thermodynamic measurements using fluorescence spectroscopy suggest that the interaction is enthalpy driven, with an overall change in free energy of binding, DeltaG = -54 kJ/mol, at room temperature. The parameters are interpreted on the basis of the structural information. The kinetics of binding suggest a diffusion-limited mechanism, whereby the peptide easily adopts a bound conformation upon interaction with the antibody. Moreover, comparative analysis with alanine-scanning results of the epitope explains the basis of selectivity for BNP over other related natriuretic peptides.
PDB ID: 3E8UDownload
MMDB ID: 75128
PDB Deposition Date: 2008/8/20
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
Mus musculus
Similar Structures:
Biological Unit for 3E8U: hexameric; determined by author and by software (PISA)
Molecular Components in 3E8U
Label Count Molecule
Proteins (6 molecules)
FAB 106.3 Heavy Chain
Molecule annotation
FAB 106.3 Light Chain
Molecule annotation
BNP Peptide Epitope
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB