7QO9

SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD and NTD (Local)

• PDB DOI: https://doi.org/10.2210/pdb7QO9/pdb
• EM Map EMD-14087: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2021-12-23 Released: 2022-01-26 
• Deposition Author(s): Ni, D., Lau, K., Turelli, P., Beckert, B., Nazarov, S., Pojer, F., Myasnikov, A., Stahlberg, H., Trono, D.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.88 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion

Ni, D., Lau, K., Turelli, P., Raclot, C., Beckert, B., Nazarov, S., Pojer, F., Myasnikov, A., Stahlberg, H., Trono, D.

(2021) Biorxiv 

• DOI: https://doi.org/10.1101/2021.12.27.474250

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 286.99 kDa 
• Atom Count: 9,180 
• Modelled Residue Count: 1,166 
• Deposited Residue Count: 2,570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,SARS-CoV-2 S Omicron Spike B.1.1.529	A, B	1,285	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth D]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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	D [auth C], E	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	F [auth A], G [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: 3.88 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Ni, D., Lau, K., Turelli, P., Beckert, B., Nazarov, S., Pojer, F., Myasnikov, A., Stahlberg, H., Trono, D.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release