7DZX | pdb_00007dzx

Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 8D2

• PDB DOI: https://doi.org/10.2210/pdb7DZX/pdb
• EM Map EMD-30918: EMDB EMDataResource

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


• Deposited: 2021-01-26 Released: 2021-06-02 
• Deposition Author(s): Liu, Y., Soh, W.T., Li, S., Kishikawa, J., Hirose, M., Kato, T., Standley, D., Okada, M., Arase, H.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.53 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies.

Liu, Y., Soh, W.T., Kishikawa, J.I., Hirose, M., Nakayama, E.E., Li, S., Sasai, M., Suzuki, T., Tada, A., Arakawa, A., Matsuoka, S., Akamatsu, K., Matsuda, M., Ono, C., Torii, S., Kishida, K., Jin, H., Nakai, W., Arase, N., Nakagawa, A., Matsumoto, M., Nakazaki, Y., Shindo, Y., Kohyama, M., Tomii, K., Ohmura, K., Ohshima, S., Okamoto, T., Yamamoto, M., Nakagami, H., Matsuura, Y., Nakagawa, A., Kato, T., Okada, M., Standley, D.M., Shioda, T., Arase, H.

(2021) Cell 184: 3452-3466.e18

• PubMed: 34139176 
• DOI: https://doi.org/10.1016/j.cell.2021.05.032
• Primary Citation of Related Structures:  
  7DZW, 7DZX, 7DZY


• PubMed Abstract: 
  

  Antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein prevent SARS-CoV-2 infection. However, the effects of antibodies against other spike protein domains are largely unknown. Here, we screened a series of anti-spike monoclonal antibodies from coronavirus disease 2019 (COVID-19) patients and found that some of antibodies against the N-terminal domain (NTD) induced the open conformation of RBD and thus enhanced the binding capacity of the spike protein to ACE2 and infectivity of SARS-CoV-2. Mutational analysis revealed that all of the infectivity-enhancing antibodies recognized a specific site on the NTD. Structural analysis demonstrated that all infectivity-enhancing antibodies bound to NTD in a similar manner. The antibodies against this infectivity-enhancing site were detected at high levels in severe patients. Moreover, we identified antibodies against the infectivity-enhancing site in uninfected donors, albeit at a lower frequency. These findings demonstrate that not only neutralizing antibodies but also enhancing antibodies are produced during SARS-CoV-2 infection.

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Organizational Affiliation: 
• Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan.
Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan.
Laboratory for CryoEM Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
Department Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
Department Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Laboratory for Supramolecular Crystallography, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
Department of Dermatology, Graduate school of Medicine, Osaka University, Osaka 565-0871, Japan.
Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Hyogo 650-0047, Japan.
Drug Discovery Research Center, HuLA immune, Inc., Osaka 565-0871, Japan.
Department of Rheumatology, Kobe City Medical Center General Hospital, Hyogo 650-0047, Japan.
Department of Clinical Research, Osaka Minami Medical Center, Kawachinagano, Osaka 586-8521, Japan.
Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
Department of Health Development and Medicine, Graduate school of Medicine, Osaka University, Osaka 565-0871, Japan.
Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
Laboratory for Supramolecular Crystallography, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
Department Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.
Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 462.49 kDa 
• Atom Count: 15,212 
• Modeled Residue Count: 3,803 
• Deposited Residue Count: 4,187 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,249	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6  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
Fab Heavy chain of enhancing antibody	D [auth H]	227	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain of enhancing antibody	E [auth L]	213	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.53 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.0.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Liu, Y., Soh, W.T., Li, S., Kishikawa, J., Hirose, M., Kato, T., Standley, D., Okada, M., Arase, H.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP19fk0108161
Japan Agency for Medical Research and Development (AMED)	Japan	JP20nf0101623
Japan Agency for Medical Research and Development (AMED)	Japan	JP20nk0101602
Japan Agency for Medical Research and Development (AMED)	Japan	JP17am0101108
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19H04808
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H05279
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H03478

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Refinement description