22PD | pdb_000022pd

Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937 Fab (local refine)

PDB DOI: https://doi.org/10.2210/pdb22PD/pdb
EM Map EMD-68583: EMDB EMDataResource

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

Deposited: 2026-01-19 Released: 2026-09-16
Deposition Author(s): Wang, X., Guo, F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Twenty-year persistence of SARS-CoV-1 immune imprinting shapes antibody responses to SARS-CoV-2 infection.

Zhang, Q., Chen, P., Guo, F., Zhou, R., Guo, R., Ge, X., Yang, Q., Xie, X., Xia, W., Fan, J., Yang, Z., Xu, Y., Huang, H., Li, J., Wang, H., Liao, H., Shi, X., Liu, N., Chen, Y., Chen, Z., Ma, J., Wang, X., Zhang, T., Zhang, L.

(2026) Immunity

PubMed: 42705227 Search on PubMed
DOI: https://doi.org/10.1016/j.immuni.2026.08.009
Primary Citation Related Structures:
22PD, 45IC, 45ID

PubMed Abstract:
Antibody imprinting is well recognized, yet its long-term dynamics and epitope specificity remain poorly understood. Here, we studied individuals sequentially infected with SARS-CoV-1 (SARS-1) and SARS-CoV-2 (SARS-2) over two decades and found durable imprinting of antibody responses following SARS-2 BF.7 breakthrough infection. Approximately 60% of isolated monoclonal antibodies were SARS-1 imprinted and targeted conserved receptor-binding domain regions, whereas 37% overcame imprinting to recognize the SARS-2 receptor-binding motif overlapping the ACE2-binding site. Notably, some SARS-1-only antibodies retained germline-like features and neutralizing activity 20 years after infection. One exceptionally imprinted broadly neutralizing antibody, THZ937, protected hamsters against contact and airborne transmission of Omicron EG.5.1, demonstrating the functional relevance of durable imprinted antibodies. Together, these findings define the remarkable longevity and molecular basis of antibody imprinting and provide insights for pan-sarbecovirus vaccine design.

Organizational Affiliation

Comprehensive AIDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China. Electronic address: zhangqi2013@mail.tsinghua.edu.cn.

Comprehensive AIDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China.

The Ministry of Education Key Laboratory of Protein Science, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.

AIDS Institute, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region.

Helixon, No. 1 Yard, Zhongguancun East Road, Haidian District, 100089 Beijing, China.

Health and Wellness, City University of Macau, Macau 999078, China.

Beijing Youan Hospital, Capital Medical University, Beijing 100069, China.

Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100730, China.

The Ministry of Education Key Laboratory of Protein Science, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Electronic Engineering, Tsinghua University, Beijing 100084, China; Institute for AI Industry Research, Tsinghua University, Beijing 100084, China. Electronic address: majianzhu@tsinghua.edu.cn.

Beijing Youan Hospital, Capital Medical University, Beijing 100069, China. Electronic address: zt_doc@ccmu.edu.cn.

Comprehensive AIDS Research Center, Pandemic Research Alliance Unit, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China. Electronic address: zhanglinqi@tsinghua.edu.cn.

Macromolecule Content

Total Structure Weight: 49.04 kDa
Atom Count: 3,378
Modeled Residue Count: 436
Deposited Residue Count: 440
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THZ937 fab heavy chain	A	128	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THZ937 fab light chain	B	112	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 BA.4 spike RBD	C	200	Severe acute respiratory syndrome coronavirus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]