9ODB

Clone 2.1 Fab in complex with chicken IgY CH2 domain (local refinement)

Summary for 9ODB

• Entry DOI: 10.2210/pdb9odb/pdb
• EMDB information: 70353
• Descriptor: chicken IgY heavy chain,Ig-like domain-containing protein, Clone 2.1 Fab heavy chain, Clone 2.1 Fab light chain, ... (4 entities in total)
• Functional Keywords: germinal center evolution, antibody, immune system
• Biological source: Gallus gallus; More
• Total number of polymer chains: 6
• Total formula weight: 218459.50

Authors

Ozorowski, G.,Alkutkar, T.,Ward, A.B. (deposition date: 2025-04-26, release date: 2025-06-11, Last modification date: 2025-07-30)

Primary citation

DeWitt, W.S.,Vora, A.A.,Araki, T.,Galloway, J.G.,Alkutkar, T.,Bortolatto, J.,Castro, T.B.R.,Dumm, W.,Jennings-Shaffer, C.,Jia, T.,Mesin, L.,Ozorowski, G.,Pae, J.,Ralph, D.K.,Bloom, J.D.,Nourmohammad, A.,Song, Y.S.,Ward, A.B.,Starr, T.N.,Matsen, F.A.,Victora, G.D.
Replaying germinal center evolution on a quantified affinity landscape.
Biorxiv, 2025

PubMed Abstract: Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition between GC B cells drives increased affinity are well established, the dynamical evolutionary features of this process remain poorly characterized. We devised an experimental evolution model in which we "replay" over one hundred instances of a clonally homogenous GC reaction and follow the selective process by assigning affinities to all cells using deep mutational scanning. Our data reveal how GCs achieve predictable evolutionary outcomes through the cumulative effects of many rounds of imperfect selection, acting on a landscape shaped heavily by somatic hypermutation (SHM) targeting biases. Using time-calibrated models, we show that apparent features of GC evolution such as permissiveness to low-affinity lineages and early plateauing of affinity are best explained by survivorship biases that distort our view of how affinity progresses over time.

PubMed: 40661619
DOI: 10.1101/2025.06.02.656870

Experimental method

ELECTRON MICROSCOPY (4 Å)