8HED | pdb_00008hed

Local refinement of the SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab

• PDB DOI: https://doi.org/10.2210/pdb8HED/pdb
• EM Map EMD-34688: EMDB EMDataResource

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


• Deposited: 2022-11-08 Released: 2023-04-26 
• Deposition Author(s): Guo, H., Gao, Y., Lu, Y., Yang, H., Ji, X.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of an RBM-targeted rabbit monoclonal antibody 9H1 neutralizing SARS-CoV-2.

Chu, X., Ding, X., Yang, Y., Lu, Y., Li, T., Gao, Y., Zheng, L., Xiao, H., Yang, T., Cheng, H., Huang, H., Liu, Y., Lou, Y., Wu, C., Chen, Y., Yang, H., Ji, X., Guo, H.

(2023) Biochem Biophys Res Commun 660: 43-49

• PubMed: 37062240 
• DOI: https://doi.org/10.1016/j.bbrc.2023.04.002
• Primary Citation Related Structures: 
  8HEB, 8HEC, 8HED


• PubMed Abstract: 
  

  The COVID-19 pandemic, caused by SARS-CoV-2, has led to over 750 million infections and 6.8 million deaths worldwide since late 2019. Due to the continuous evolution of SARS-CoV-2, many significant variants have emerged, creating ongoing challenges to the prevention and treatment of the pandemic. Therefore, the study of antibody responses against SARS-CoV-2 is essential for the development of vaccines and therapeutics. Here we perform single particle cryo-electron microscopy (cryo-EM) structure determination of a rabbit monoclonal antibody (RmAb) 9H1 in complex with the SARS-CoV-2 wild-type (WT) spike trimer. Our structural analysis shows that 9H1 interacts with the receptor-binding motif (RBM) region of the receptor-binding domain (RBD) on the spike protein and by directly competing with angiotensin-converting enzyme 2 (ACE2), it blocks the binding of the virus to the receptor and achieves neutralization. Our findings suggest that utilizing rabbit-derived mAbs provides valuable insights into the molecular interactions between neutralizing antibodies and spike proteins and may also facilitate the development of therapeutic antibodies and expand the antibody library.

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Organizational Affiliation: 
• The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China.
Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, 210008, China; School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu, 210094, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
Yurogen Biosystem LLC, Wuhan, Hubei, 430075, China.
Institute of Viruses and Infectious Diseases, Nanjing University, Nanjing, Jiangsu, 210008, China.
Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, 210008, China; Institute of Viruses and Infectious Diseases, Nanjing University, Nanjing, Jiangsu, 210008, China. Electronic address: [e-mail].
The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China; Institute of Viruses and Infectious Diseases, Nanjing University, Nanjing, Jiangsu, 210008, China. Electronic address: [e-mail].
The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 47.3 kDa 
• Atom Count: 3,318 
• Modeled Residue Count: 427 
• Deposited Residue Count: 427 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth B]	200	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: 2		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
rabbit antibody 9H1 light chain	B [auth F]	110	Oryctolagus cuniculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
rabbit antibody 9H1 heavy chain	C [auth G]	117	Oryctolagus cuniculus	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth O]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Guo, H., Gao, Y., Lu, Y., Yang, H., Ji, X.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-02
  Changes: Data collection