Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 387.61 kDa 
• Atom Count: 25,629 
• Modelled Residue Count: 3,189 
• Deposited Residue Count: 3,399 
• Unique protein chains: 1

 7WG8

Delta Spike Trimer(3 RBD Down)

• PDB DOI:  https://doi.org/10.2210/pdb7WG8/pdb
• EM Map EMD-32480: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-12-28 Released: 2022-06-22 
• Deposition Author(s): Cui, Z.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

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

Literature

Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron.

Cui, Z., Liu, P., Wang, N., Wang, L., Fan, K., Zhu, Q., Wang, K., Chen, R., Feng, R., Jia, Z., Yang, M., Xu, G., Zhu, B., Fu, W., Chu, T., Feng, L., Wang, Y., Pei, X., Yang, P., Xie, X.S., Cao, L., Cao, Y., Wang, X.

(2022) Cell 185: 860-871.e13

• PubMed: 35120603 
• DOI: https://doi.org/10.1016/j.cell.2022.01.019
• Primary Citation of Related Structures:  
  7WG6, 7WG7, 7WG8, 7WG9, 7WGB, 7WGC


• PubMed Abstract: 
  

The SARS-CoV-2 Omicron variant with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the spike (S) from Omicron reveals amino acid substitutions forging interactions that stably maintain an active conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of the viral fusion step. Alterations in local conformation, charge, and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Structure of the Omicron S bound with human ACE2, together with the analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members, as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies, sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.

---

Organizational Affiliation: 

CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth A], C	1,133	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 9  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G, H, I	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	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth A], J [auth B], JA [auth C], K [auth B], KA [auth C], L [auth B], LA [auth C], M [auth B], MA [auth C], N [auth B], NA [auth C], O [auth B], OA [auth C], P [auth B], PA [auth C], Q [auth B], QA [auth C], R [auth B], RA [auth C], S [auth B], SA [auth C], T [auth B], TA [auth C], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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: 2022-06-22 
Deposition Author(s): Cui, Z.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release