7XCK

Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb7XCK/pdb
• EM Map EMD-33123: 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., Xie, Y.F., Liu, S.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 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 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 78.79 kDa 
• Atom Count: 5,488 
• Modelled Residue Count: 704 
• Deposited Residue Count: 713 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 heavy chain	A	230	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 light chain	B	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth M]	269	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 16  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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 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., Xie, Y.F., Liu, S.

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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
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary