6PYD image
Entry Detail
PDB ID:
6PYD
Keywords:
Title:
Structure of 3E9 antibody Fab bound to marinobufagenin
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2019-07-29
Release Date:
2019-12-25
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:3E9 anti-marinobufagenin antibody Fab heavy chain, recloned with human IgG4 C region
Chain IDs:A (auth: H), C (auth: A)
Chain Length:222
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:3E9 antibody Fab light chain
Chain IDs:B (auth: L), D (auth: B)
Chain Length:219
Number of Molecules:2
Biological Source:Mus musculus
Ligand Molecules
Primary Citation

Abstact

We describe a Kappa-on-Heavy (KoH) mouse that produces a class of highly diverse, fully human, antibody-like agents. This mouse was made by replacing the germline variable sequences of both the Ig heavy-chain (IgH) and Ig kappa (IgK) loci with the human IgK germline variable sequences, producing antibody-like molecules with an antigen binding site made up of 2 kappa variable domains. These molecules, named KoH bodies, structurally mimic naturally existing Bence-Jones light-chain dimers in their variable domains and remain wild-type in their antibody constant domains. Unlike artificially diversified, nonimmunoglobulin alternative scaffolds (e.g., DARPins), KoH bodies consist of a configuration of normal Ig scaffolds that undergo natural diversification in B cells. Monoclonal KoH bodies have properties similar to those of conventional antibodies but exhibit an enhanced ability to bind small molecules such as the endogenous cardiotonic steroid marinobufagenin (MBG) and nicotine. A comparison of crystal structures of MBG bound to a KoH Fab versus a conventional Fab showed that the KoH body has a much deeper binding pocket, allowing MBG to be held 4 Å further down into the combining site between the 2 variable domains.

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Primary Citation of related structures