7Y7K | pdb_00007y7k

SARS-CoV-2 RBD in complex with 1F Fab

• PDB DOI: https://doi.org/10.2210/pdb7Y7K/pdb
• EM Map EMD-33668: 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: 2022-06-22 Released: 2023-02-22 
• Deposition Author(s): Zhao, S., Liu, F., Yang, X., Zhong, G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A core epitope targeting antibody of SARS-CoV-2.

Zhao, S., Liu, F., Qiu, S., Lan, Q., Wu, Y., Xu, W., Ke, J., Yang, J., Liu, X., Wang, K., Guo, H., Xia, S., Zhang, F., Wang, J., Hu, X., Lu, L., Jiang, S., Zhao, S., Liu, L., Xie, Y., Yang, X., Wang, H., Zhong, G.

(2023) Protein Cell 14: 74-78

• PubMed: 36726762 
• DOI: https://doi.org/10.1093/procel/pwac042
• Primary Citation Related Structures: 
  7Y7J, 7Y7K

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Biosafety Level 3 Laboratory, Fudan University, Shanghai 200032, China.
Department of Hepatobiliary Surgery, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, The University of Science and Technology of China, Hefei 230001, China.
Department of Pulmonary and Critical Care Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, The University of Science and Technology of China, Hefei 230026, China.
Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, The University of Sciences and Technology of China, Hefei 230001, China.

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: 46.45 kDa 
• Atom Count: 2,942 
• Modeled Residue Count: 422 
• Deposited Residue Count: 422 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	179	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1F VH	B	132	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
1F VL	C	111	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Zhao, S., Liu, F., Yang, X., Zhong, G.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary