7F3Q | pdb_00007f3q

SARS-CoV-2 RBD in complex with A5-10 Fab and A34-2 Fab

• PDB DOI: https://doi.org/10.2210/pdb7F3Q/pdb
• EM Map EMD-31434: EMDB EMDataResource

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


• Deposited: 2021-06-16 Released: 2022-06-22 
• Deposition Author(s): Dou, Y., Wang, X., Liu, P., Lu, B., Wang, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Development of neutralizing antibodies against SARS-CoV-2, using a high-throughput single-B-cell cloning method.

Dou, Y., Xu, K., Deng, Y.Q., Jia, Z., Lan, J., Xu, X., Zhang, G., Cao, T., Liu, P., Wang, X., Wang, X., Xu, L., Du, P., Qin, C.F., Liu, H., Li, Y., Wu, G., Wang, K., Lu, B.

(2023) Antib Ther 6: 76-86

• PubMed: 37077472 
• DOI: https://doi.org/10.1093/abt/tbad002
• Primary Citation Related Structures: 
  7F3Q


• PubMed Abstract: 
  

  Rapid and efficient strategies are needed to discover neutralizing antibodies (nAbs) from B cells derived from virus-infected patients. Here, we report a high-throughput single-B-cell cloning method for high-throughput isolation of nAbs targeting diverse epitopes on the SARS-CoV-2-RBD (receptor binding domain) from convalescent COVID-19 patients. This method is simple, fast and highly efficient in generating SARS-CoV-2-neutralizing antibodies from COVID-19 patients' B cells. Using this method, we have developed multiple nAbs against distinct SARS-CoV-2-RBD epitopes. CryoEM and crystallography revealed precisely how they bind RBD. In live virus assay, these nAbs are effective in blocking viral entry to the host cells. This simple and efficient method may be useful in developing human therapeutic antibodies for other diseases and next pandemic.

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Organizational Affiliation: 
• School of Pharmaceutical Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, AMMS, Beijing 100071, China.
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Vazyme Biotech Co., Ltd., Nanjing, China.
Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
Shanxi Provincial Key Laboratory of Kidney Disease, The Fifth Hospital of Shanxi Medical University, Taiyuan 030012, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 234.01 kDa 
• Atom Count: 8,003 
• Modeled Residue Count: 1,050 
• Deposited Residue Count: 2,138 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,273	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of A34-2 Fab	B [auth H]	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of A34-2 Fab	C [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of A5-10 Fab	D [auth C]	227	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of A5-10 Fab	E [auth B]	205	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES (Subject of Investigation/LOI)	G [auth H]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Dou, Y., Wang, X., Liu, P., Lu, B., Wang, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary