7M8J | pdb_00007m8j

SARS-CoV-2 S-NTD + Fab CM25

• PDB DOI: https://doi.org/10.2210/pdb7M8J/pdb
• EM Map EMD-23717: EMDB EMDataResource

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


• Deposited: 2021-03-29 Released: 2021-05-19 
• Deposition Author(s): Johnson, N.V., Mclellan, J.S.
• 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: 3.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes.

Voss, W.N., Hou, Y.J., Johnson, N.V., Delidakis, G., Kim, J.E., Javanmardi, K., Horton, A.P., Bartzoka, F., Paresi, C.J., Tanno, Y., Chou, C.W., Abbasi, S.A., Pickens, W., George, K., Boutz, D.R., Towers, D.M., McDaniel, J.R., Billick, D., Goike, J., Rowe, L., Batra, D., Pohl, J., Lee, J., Gangappa, S., Sambhara, S., Gadush, M., Wang, N., Person, M.D., Iverson, B.L., Gollihar, J.D., Dye, J.M., Herbert, A.S., Finkelstein, I.J., Baric, R.S., McLellan, J.S., Georgiou, G., Lavinder, J.J., Ippolito, G.C.

(2021) Science 372: 1108-1112

• PubMed: 33947773 
• DOI: https://doi.org/10.1126/science.abg5268
• Primary Citation Related Structures: 
  7M8J


• PubMed Abstract: 
  

  The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.

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Organizational Affiliation: 
• Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
Department of Chemistry, The University of Texas at Austin, Austin, TX, USA.
U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
CCDC Army Research Laboratory-South, The University of Texas at Austin, Austin, TX, USA.
Biomedicine Design, Pfizer, Cambridge, MA, USA.
Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Tulane National Primate Research Center Department of Microbiology 18703 Three Rivers Road Covington, LA, USA.
Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA.
Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. [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: microscopy

Macromolecule Content 

• Total Structure Weight: 53.77 kDa 
• Atom Count: 3,517 
• Modeled Residue Count: 453 
• Deposited Residue Count: 486 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	257	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CM25 Fab - Heavy Chain	B [auth H]	120	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CM25 Fab - Light Chain	C [auth L]	109	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Johnson, N.V., Mclellan, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI127521

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2021-06-16
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary