7KM6

APOBEC3B antibody 5G7 Fv-clasp

Summary for 7KM6

• Entry DOI: 10.2210/pdb7km6/pdb
• Descriptor: 5G7 human monoclonal FAB light chain, 5G7 human monoclonal FAB heavy chain, 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: immune system
• Biological source: Homo sapiens; More
• Total number of polymer chains: 4
• Total formula weight: 78306.13

Authors

Tang, H.,Shi, K.,Aihara, H. (deposition date: 2020-11-02, release date: 2021-05-12, Last modification date: 2024-10-09)

Primary citation

Tang, H.,Demir, O.,Kurniawan, F.,Brown, W.L.,Shi, K.,Moeller, N.H.,Carpenter, M.A.,Belica, C.,Orellana, K.,Du, G.,LeBeau, A.M.,Amaro, R.E.,Harris, R.S.,Aihara, H.
Structural Characterization of a Minimal Antibody against Human APOBEC3B.
Viruses, 13:-, 2021

PubMed Abstract: APOBEC3B (A3B) is one of seven human APOBEC3 DNA cytosine deaminases that restrict viral infections as part of the overall innate immune response, but it also plays a major role in tumor evolution by mutating genomic DNA. Given the importance of A3B as a restriction factor of viral infections and as a driver of multiple human cancers, selective antibodies against A3B are highly desirable for its specific detection in various research and possibly diagnostic applications. Here, we describe a high-affinity minimal antibody, designated 5G7, obtained via a phage display screening against the C-terminal catalytic domain (ctd) of A3B. 5G7 also binds APOBEC3A that is highly homologous to A3Bctd but does not bind the catalytic domain of APOBEC3G, another Z1-type deaminase domain. The crystal structure of 5G7 shows a canonical arrangement of the heavy and light chain variable domains, with their complementarity-determining region (CDR) loops lining an antigen-binding cleft that accommodates a pair of α-helices. To understand the mechanism of A3Bctd recognition by 5G7, we used the crystal structures of A3Bctd and 5G7 as templates and computationally predicted the A3B-5G7 complex structure. Stable binding poses obtained by the simulation were further tested by site-directed mutagenesis and in vitro binding analyses. These studies mapped the epitope for 5G7 to a portion of C-terminal α6 helix of A3Bctd, with Arg374 playing an essential role. The same region of A3Bctd was used previously as a peptide antigen for generating a rabbit monoclonal antibody (mAb 5210-87-13), suggesting that this region is particularly immunogenic and that these antibodies from very different origins may share similar binding modes. Our studies provide a platform for the development of selective antibodies against A3B and other APOBEC3 family enzymes.

PubMed: 33921405
DOI: 10.3390/v13040663

Experimental method

X-RAY DIFFRACTION (1.67 Å)