9WLB

Local refinement region of SARS-CoV-2 spike RBD in complex with antibodies S309 and CT1-1.

Summary for 9WLB

• Entry DOI: 10.2210/pdb9wlb/pdb
• EMDB information: 66052
• Descriptor: S309 Fab light chain, S309 Fab heavy chain, CT1-1 Fab heavy chain, ... (6 entities in total)
• Functional Keywords: sars-cov-2, rbd, fab, viral protein/immune system, viral protein-immune system complex
• Biological source: Homo sapiens; More
• Total number of polymer chains: 5
• Total formula weight: 87515.11

Authors

Jiang, Y.,Sun, H.,Zheng, Q.,Li, S. (deposition date: 2025-09-02, release date: 2026-06-03, Last modification date: 2026-07-01)

Primary citation

Zhou, L.,Yu, Z.,Lin, S.,Jiang, Y.,Gao, J.,Ma, Y.,Jiang, W.,Liang, S.,Chen, Y.,Zhang, Y.,Lin, Y.,Liang, M.,Dai, J.,Zhang, L.,Xiao, Y.,Li, T.,Kong, Z.,Liu, Q.,He, S.,Wu, Y.,Yuan, Q.,Liu, F.,Zhang, J.,Zheng, Q.,Yu, H.,Gu, Y.,Li, S.,Xia, N.
Public antibody clonotypes and deep learning identify SARS-CoV-2 and HIV broadly neutralizing antibodies in immune repertoires.
Cell Rep, 45:117582-117582, 2026

PubMed Abstract: Broadly neutralizing antibodies (bnAbs) are essential for the development of vaccines and therapeutics against rapidly evolving pathogens like HIV and SARS-CoV-2, yet traditional discovery methods remain technically challenging and time consuming. Here, we introduce ClonoDeep, an AI-powered platform that integrates public antibody clonotypes with a sequence-based deep learning model to directly identify bnAbs from a large-scale immune repertoire, independent of antigen-specific immunization. Applied to SARS-CoV-2 repertoires, ClonoDeep identified 18 clonotype-derived antibody candidates; 83% of the candidates were neutralizing antibodies, and 8 of these antibodies demonstrated broad neutralization across variants. Structural analysis revealed that somatic hypermutations at HCDR3 His107/Gly109 are key enhancers of the binding affinity and neutralizing breadth. Extending to HIV, ClonoDeep uncovered three previously unreported bnAbs from non-HIV cohorts, indicating that rare bnAb-like precursors exist in non-HIV cohort repertoires. ClonoDeep establishes a high-throughput computational approach for mining neutralizing antibodies from antibody repertoires shaped by non-pathogen-specific immunity and provides design principles to guide vaccine strategies against genetically diverse pathogens.

PubMed: 42319828
DOI: 10.1016/j.celrep.2026.117582

Experimental method

ELECTRON MICROSCOPY (3.74 Å)