7WP5

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

• PDB DOI: https://doi.org/10.2210/pdb7WP5/pdb
• EM Map EMD-32669: 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: 2022-07-13 
• 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: 3.90 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 of 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].

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: 48.04 kDa 
• Atom Count: 3,340 
• Modelled Residue Count: 425 
• Deposited Residue Count: 431 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VacW-209 light chain	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
Spikeprotein S1	C [auth F]	189	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15  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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
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: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary