8D5A | pdb_00008d5a

Middle state of SARS-CoV-2 BA.2 variant spike protein

• PDB DOI: https://doi.org/10.2210/pdb8D5A/pdb
• EM Map EMD-27207: EMDB EMDataResource

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


• Deposited: 2022-06-04 Released: 2023-06-07 
• Deposition Author(s): Zhang, J., Tang, W.C., Gao, H.L., Shi, W., Peng, H.Q., Volloch, S.R., Xiao, T.S., Chen, B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein.

Zhang, J., Tang, W., Gao, H., Lavine, C.L., Shi, W., Peng, H., Zhu, H., Anand, K., Kosikova, M., Kwon, H.J., Tong, P., Gautam, A., Rits-Volloch, S., Wang, S., Mayer, M.L., Wesemann, D.R., Seaman, M.S., Lu, J., Xiao, T., Xie, H., Chen, B.

(2023) Nat Struct Mol Biol 30: 980-990

• PubMed: 37430064 
• DOI: https://doi.org/10.1038/s41594-023-01023-6
• Primary Citation Related Structures: 
  8D55, 8D56, 8D5A


• PubMed Abstract: 
  

  The Omicron subvariant BA.2 has become the dominant circulating strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in many countries. Here, we have characterized structural, functional and antigenic properties of the full-length BA.2 spike (S) protein and compared replication of the authentic virus in cell culture and an animal model with previously prevalent variants. BA.2 S can fuse membranes slightly more efficiently than Omicron BA.1, but still less efficiently than other previous variants. Both BA.1 and BA.2 viruses replicated substantially faster in animal lungs than the early G614 (B.1) strain in the absence of pre-existing immunity, possibly explaining the increased transmissibility despite their functionally compromised spikes. As in BA.1, mutations in the BA.2 S remodel its antigenic surfaces, leading to strong resistance to neutralizing antibodies. These results suggest that both immune evasion and replicative advantage may contribute to the heightened transmissibility of the Omicron subvariants.

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Organizational Affiliation: 
• Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA, USA.
Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital; Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA.
Codex BioSolutions, Inc., Rockville, MD, USA.
The Harvard Cryo-EM Center for Structural Biology, Boston, MA, USA.
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA.
Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. [e-mail].
Department of Pediatrics, Harvard Medical School, Boston, MA, USA. [e-mail].
Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, USA. [e-mail].
Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. [e-mail].
Department of Pediatrics, Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 454.15 kDa 
• Atom Count: 27,711 
• Modeled Residue Count: 3,365 
• Deposited Residue Count: 3,915 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 28  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 16		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], CA [auth c], D, EA [auth e], F, FA [auth f], H, I, K, L, M, P, R, S, U, V, W, Z	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], E, G, N, O, Q, X, Y	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth d], J, T	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Zhang, J., Tang, W.C., Gao, H.L., Shi, W., Peng, H.Q., Volloch, S.R., Xiao, T.S., Chen, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI147884
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI141002
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI127193
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI39538
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI165072
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI69619

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2023-07-12
  Changes: Database references, Other
• Version 1.2: 2023-07-26
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary