9JEB

Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv N1

Summary for 9JEB

• Entry DOI: 10.2210/pdb9jeb/pdb
• Descriptor: N1 scFv, Spike protein S1, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: sars-cov-2, rbd, antibody, scfv, viral protein, viral protein-immune system complex, viral protein/immune system
• Biological source: Homo sapiens; More
• Total number of polymer chains: 4
• Total formula weight: 97173.05

Authors

Guo, K.,Zhang, N.,Guo, Y. (deposition date: 2024-09-03, release date: 2025-09-03, Last modification date: 2026-05-20)

Primary citation

Terekhov, S.S.,Ivanisenko, N.V.,Zhang, N.,Mokrushina, Y.A.,Nolde, D.E.,Lomakin, Y.A.,Zalevsky, A.,Ovchinnikova, L.A.,Malabuiok, D.M.,Baranova, M.N.,Shashkova, T.,Aliper, E.,Zhang, M.,Guo, K.,Duga, S.,Akhmetyanov, N.,Mamontov, S.,Smirnova, A.O.,Mamedov, I.,Bobik, T.V.,Kostin, N.N.,Chernov, A.S.,Eliseev, I.E.,Yaroshevich, I.,Boitsov, V.M.,Stepanov, A.V.,Zhang, D.,Efremov, R.G.,Smirnov, I.V.,Kardymon, O.,Zhang, H.,Guo, Y.,Lerner, R.,Gabibov, A.G.,Kornberg, R.D.
Mining antibody functionality via AI-guided structural landscape profiling.
Nat Commun, 17:-, 2026

PubMed Abstract: Despite substantial progress in single-cell screening techniques, antibody (Ab) repertoires still remain enigmatic. Here we show that Ab sequences can be linked to their functionality by using big data obtained from high-throughput sequencing. Using the expansive SARS-CoV-2 pandemic data, we develop an AI-based method to reveal the neutralization potential of Ab repertoires. We employ machine learning to process public 3D structural data of Ab-RBD complexes and create a comprehensive tool, RBD-AIM (https://rbdaim.2a2i.org/), for high-throughput prediction of structural Ab epitopes based on Ab sequence. Using RBD-AIM, we analyze the local big data sources to evaluate the functional biodiversity of native B cell repertoires raised after vaccination and reconstructed in a yeast display system using single-cell microfluidics. This pipeline allows for rapid isolation of neutralizing Abs that promote the survival of transgenic hACE2+ mice in lethal models of SARS-CoV-2 infection. We believe that the AI-guided sequence-functionality link can be successfully employed for further high-throughput discovery of therapeutic Abs and functional analysis of Ab repertoires.

PubMed: 41833937
DOI: 10.1038/s41467-026-70553-6

Experimental method

X-RAY DIFFRACTION (2.3 Å)