7TLY | pdb_00007tly

SARS-CoV-2 S B.1.1.529 Omicron variant (RBD + S309 Local Refinement)

• PDB DOI: https://doi.org/10.2210/pdb7TLY/pdb
• EM Map EMD-25990: EMDB EMDataResource

• Classification: VIRUS/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Mutation(s): Yes 


• Deposited: 2022-01-19 Released: 2022-02-02 
• Deposition Author(s): McCallum, M., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement.

McCallum, M., Czudnochowski, N., Rosen, L.E., Zepeda, S.K., Bowen, J.E., Walls, A.C., Hauser, K., Joshi, A., Stewart, C., Dillen, J.R., Powell, A.E., Croll, T.I., Nix, J., Virgin, H.W., Corti, D., Snell, G., Veesler, D.

(2022) Science 375: 864-868

• PubMed: 35076256 
• DOI: https://doi.org/10.1126/science.abn8652
• Primary Citation Related Structures: 
  7TLY, 7TLZ, 7TM0, 7TN0


• PubMed Abstract: 
  

  The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Vir Biotechnology, San Francisco, CA 94158, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK.
Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA.
Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.

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: electron microscopy

Macromolecule Content 

• Total Structure Weight: 179.46 kDa 
• Atom Count: 3,105 
• Modeled Residue Count: 408 
• Deposited Residue Count: 1,614 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 Fab heavy chain	A	126	Homo sapiens	Mutation(s): 0

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth I]	1,274	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 40  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	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): McCallum, M., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2022-02-09
  Changes: Database references
• Version 1.2: 2022-03-09
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary