7WP0 | pdb_00007wp0

Cryo-EM structure of SARS-CoV-2 Delta S6P trimer in complex with neutralizing antibody VacW-209 (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb7WP0/pdb
• EM Map EMD-32665: EMDB EMDataResource

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-01-22 Released: 2022-07-20 
• Deposition Author(s): Zheng, Q., Sun, H., Ju, B., Zhang, Z., Li, S., Xia, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209.

Ju, B., Zheng, Q., Guo, H., Fan, Q., Li, T., Song, S., Sun, H., Shen, S., Zhou, X., Xue, W., Cui, L., Zhou, B., Li, S., Xia, N., Zhang, Z.

(2022) Cell Res 32: 491-494

• PubMed: 35260792 
• DOI: https://doi.org/10.1038/s41422-022-00638-6
• Primary Citation Related Structures: 
  7WON, 7WP0, 7WP1, 7WP2, 7WP5

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Organizational Affiliation: 
• Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China. [e-mail].
Guangdong Key laboratory for anti-infection Drug Quality Evaluation, Shenzhen, Guangdong, China. [e-mail].
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, Fujian, China.
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China.
Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China.
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, Fujian, China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China. [e-mail].
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, Fujian, China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, China. [e-mail].
Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China. [e-mail].
Guangdong Key laboratory for anti-infection Drug Quality Evaluation, Shenzhen, Guangdong, China. [e-mail].
Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, Guangdong, China. [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.

Macromolecule Content 

• Total Structure Weight: 47.61 kDa 
• Atom Count: 3,174 
• Modeled Residue Count: 407 
• Deposited Residue Count: 431 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IG c335_light_IGLV1-40_IGLJ3	A [auth L]	111	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for A0A5C2GQT9 (Homo sapiens) Explore A0A5C2GQT9  Go to UniProtKB:  A0A5C2GQT9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VacW-209 heavy chain	B [auth H]	131	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth F]	189	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2  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 (Subject of Investigation/LOI)	D [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.71 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: 2022-07-20 
Deposition Author(s): Zheng, Q., Sun, H., Ju, B., Zhang, Z., Li, S., Xia, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary
• Version 1.2: 2025-06-25
  Changes: Data collection