7N8I | pdb_00007n8i

SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 (Local Refinement of the NTD/S2L20)

• PDB DOI: https://doi.org/10.2210/pdb7N8I/pdb
• EM Map EMD-24237: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-06-14 Released: 2021-07-14 
• Deposition Author(s): McCallum, M., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

Literature

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern.

McCallum, M., Bassi, J., De Marco, A., Chen, A., Walls, A.C., Di Iulio, J., Tortorici, M.A., Navarro, M.J., Silacci-Fregni, C., Saliba, C., Sprouse, K.R., Agostini, M., Pinto, D., Culap, K., Bianchi, S., Jaconi, S., Cameroni, E., Bowen, J.E., Tilles, S.W., Pizzuto, M.S., Guastalla, S.B., Bona, G., Pellanda, A.F., Garzoni, C., Van Voorhis, W.C., Rosen, L.E., Snell, G., Telenti, A., Virgin, H.W., Piccoli, L., Corti, D., Veesler, D.

(2021) Science 373: 648-654

• PubMed: 34210893 
• DOI: https://doi.org/10.1126/science.abi7994
• Primary Citation Related Structures: 
  7N8H, 7N8I


• PubMed Abstract: 
  

  A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal domain (NTD), and L452R in the receptor-binding domain (RBD). Plasma from individuals vaccinated with a Wuhan-1 isolate-based messenger RNA vaccine or from convalescent individuals exhibited neutralizing titers that were reduced 2- to 3.5-fold against the B.1.427/B.1.429 variant relative to wild-type pseudoviruses. The L452R mutation reduced neutralizing activity in 14 of 34 RBD-specific monoclonal antibodies (mAbs). The S13I and W152C mutations resulted in total loss of neutralization for 10 of 10 NTD-specific mAbs because the NTD antigenic supersite was remodeled by a shift of the signal peptide cleavage site and the formation of a new disulfide bond, as revealed by mass spectrometry and structural studies.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
Vir Biotechnology, San Francisco, CA 94158, USA.
Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.
Independent physician, 6828 Balerna, Switzerland.
Clinical Research Unit, Clinica Luganese Moncucco, 6900 Lugano, Switzerland.
Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland.
Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland. [e-mail] [e-mail] [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. [e-mail] [e-mail] [e-mail].

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: immunoprecipitation

Macromolecule Content 

• Total Structure Weight: 167.74 kDa 
• Atom Count: 3,600 
• Modeled Residue Count: 445 
• Deposited Residue Count: 1,504 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S2L20 Fab Light Chain Variable Region	A [auth L]	106	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S2L20 Fab Heavy Chain Variable Region	B [auth H]	121	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth A]	1,277	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
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P0DTC2-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A], G [auth A], H [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: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): McCallum, M., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2021-08-18
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary