8BS8

Bovine naive ultralong antibody AbD08 collected at 100K

Summary for 8BS8

• Entry DOI: 10.2210/pdb8bs8/pdb
• Descriptor: Heavy chain, Light chain, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total)
• Functional Keywords: ultralong, immunoglobulin, naive, immune system
• Biological source: Bos taurus (cattle); More
• Total number of polymer chains: 2
• Total formula weight: 58010.73

Authors

Clarke, J.D.,Douangamath, A.,Mikolajek, H.,Stuart, D.I.,Owens, R.J. (deposition date: 2022-11-24, release date: 2023-05-24, Last modification date: 2024-07-17)

Primary citation

Clarke, J.D.,Douangamath, A.,Mikolajek, H.,Bonnet-Di Placido, M.,Ren, J.,Fry, E.E.,Stuart, D.I.,Hammond, J.A.,Owens, R.J.
The impact of exchanging the light and heavy chains on the structures of bovine ultralong antibodies.
Acta Crystallogr.,Sect.F, 80:154-163, 2024

PubMed Abstract: The third complementary-determining regions of the heavy-chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form β-ribbon stalks that protrude from the surface of the antibody with a disulfide cross-linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B-cell sequencing, has been determined to 1.6 Å resolution. By swapping the D08 native light chain with that of an unrelated antigen-unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallographic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing.

PubMed: 38958188
DOI: 10.1107/S2053230X2400606X

Experimental method

X-RAY DIFFRACTION (1.59 Å)