9JEB | pdb_00009jeb

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

• PDB DOI: https://doi.org/10.2210/pdb9JEB/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Trichoplusia
• Mutation(s): No 


• Deposited: 2024-09-03 Released: 2025-09-03 
• Deposition Author(s): Guo, K., Zhang, N., Guo, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Mining antibody functionality via AI-guided structural landscape profiling.

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.

(2026) Nat Commun 

• PubMed: 41833937 
• DOI: https://doi.org/10.1038/s41467-026-70553-6
• Primary Citation Related Structures: 
  9JEB


• 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.

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Organizational Affiliation: 
• Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Bioinformatics research group, AXXX, Moscow, Russia.
State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.
Alferov University, Saint Petersburg, Russia.
Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China. [e-mail].
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia. [e-mail].
Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.17 kDa 
• Atom Count: 7,532 
• Modeled Residue Count: 858 
• Deposited Residue Count: 888 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N1 scFv	A, C	247	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B, D	197	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.399	α = 90
b = 190.399	β = 90
c = 60.138	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Guo, K., Zhang, N., Guo, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFE0200400
National Natural Science Foundation of China (NSFC)	China	32271256

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release
  
• Version 1.1: 2026-04-01
  Changes: Database references