7XCP | pdb_00007xcp

Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 Fab

• PDB DOI: https://doi.org/10.2210/pdb7XCP/pdb
• EM Map EMD-33125: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Mammalian expression vector EGFP-MCS-pcDNA3.1
• Mutation(s): Yes 


• Deposited: 2022-03-24 Released: 2022-08-31 
• Deposition Author(s): Zhao, Z., Qi, J., Gao, F.G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 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: 4958-4958

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 139.9 kDa 
• Atom Count: 8,261 
• Modeled Residue Count: 1,017 
• Deposited Residue Count: 1,229 
• Unique protein chains: 4

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, UNQ868/PRO1885 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: Q9BYF1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of 304 Fab	C [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Lignt chain of 304 Fab	D [auth L]	215	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth 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)	F [auth A], G [auth A], H [auth A], J [auth A], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 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: 2022-08-31 
Deposition Author(s): Zhao, Z., Qi, J., Gao, F.G.

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

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-02
  Changes: Data collection