7XCI

Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with human ACE2 ectodomain (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb7XCI/pdb
• EM Map EMD-33121: EMDB EMDataResource

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


• Deposited: 2022-03-24 Released: 2022-08-31 
• Deposition Author(s): Gao, G.F., Qi, J.X., Zhao, Z.N., Liu, S., Xie, Y.F.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape

Zhao, Z., Zhou, J., Tian, M., Huang, M., Liu, S., Xie, Y., Han, P., Bai, C., Han, P., Zheng, A., Fu, L., Gao, Y., Peng, Q., Li, Y., Chai, Y., Zhang, Z., Zhao, X., Song, H., Qi, J., Wang, Q., Wang, P., Gao, G.F.

(2022) Nat Commun 13: 4958

• DOI: https://doi.org/10.1038/s41467-022-32665-7

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 93.02 kDa 
• Atom Count: 6,547 
• Modelled Residue Count: 791 
• Deposited Residue Count: 791 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	596	Homo sapiens	Mutation(s): 0  Gene Names: ACE2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	195	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

Oligosaccharides

Help

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Gao, G.F., Qi, J.X., Zhao, Z.N., Liu, S., Xie, Y.F.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release