9PMT

Structure of an anti-VHH fab fragment bound to nanobody Nb33

Summary for 9PMT

• Entry DOI: 10.2210/pdb9pmt/pdb
• Descriptor: Anti-VHH fab Heavy Chain, Anti-VHH fab Light Chain, Nanobody Nb33, ... (4 entities in total)
• Functional Keywords: antibody, fab, fab fragment, nanobody, immune system
• Biological source: Oryctolagus cuniculus; More
• Total number of polymer chains: 3
• Total formula weight: 64989.57

Authors

Srinivasan, K.,Wan, Y.,Manglik, A. (deposition date: 2025-07-18, release date: 2026-05-06, Last modification date: 2026-05-20)

Primary citation

Wan, Y.,Liang, J.,Dai, Y.,Srinivasan, K.,Billesbolle, C.,Zhu, J.F.,Shin, J.E.,Paul, S.,Marks, D.,Song, Y.S.,Myers, B.R.,Koehl, A.,Manglik, A.
Hypervariable loop profiling decodes sequence determinants of antibody stability.
Nat.Struct.Mol.Biol., 2026

PubMed Abstract: Antibody folding and aggregation are major challenges in the development of relevant reagents and therapeutics. Antibodies face a biophysical trade-off; the immense diversity in complementarity-determining regions (CDRs), which is crucial for broad antigen recognition, comes at the cost of folding stability. How CDR sequences influence antibody folding remains poorly understood because of their sequence diversity and lack of large-scale data. Here we develop a high-throughput 'deep loop profiling' approach to quantify folding fitness across millions of diverse CDRs. Machine learning models trained on this dataset predict folding propensity directly from sequence and identify interpretable residue-level rules that reveal CDR1 and CDR2 as key folding determinants. Using these insights, we rescue two unstable nanobodies, including an aggregation-prone SARS-CoV-2 binder and a G-protein-coupled receptor-targeting intrabody, and build next-generation synthetic libraries enriched for biophysically optimized nanobodies. This approach provides a scalable framework for understanding and engineering folding competence in antibody-based scaffolds.

PubMed: 42062516
DOI: 10.1038/s41594-026-01804-9

Experimental method

X-RAY DIFFRACTION (2.26 Å)