9II9 | pdb_00009ii9

Crystal structure of SARS-CoV-2 neutralizing antibody K4-66


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.288 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 
    0.264 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Induction of IGHV3-53 public antibodies with broadly neutralising activity against SARS-CoV-2 including Omicron subvariants in a Delta breakthrough infection case.

Kuwata, T.Kaku, Y.Biswas, S.Matsumoto, K.Shimizu, M.Kawanami, Y.Uraki, R.Okazaki, K.Minami, R.Nagasaki, Y.Nagashima, M.Yoshida, I.Sadamasu, K.Yoshimura, K.Ito, M.Kiso, M.Yamayoshi, S.Imai, M.Ikeda, T.Sato, K.Toyoda, M.Ueno, T.Inoue, T.Tanaka, Y.Kimura, K.T.Hashiguchi, T.Sugita, Y.Noda, T.Morioka, H.Kawaoka, Y.Matsushita, S.

(2024) EBioMedicine 110: 105439-105439

  • DOI: https://doi.org/10.1016/j.ebiom.2024.105439
  • Primary Citation of Related Structures:  
    9II9

  • PubMed Abstract: 

    Emergence of SARS-CoV-2 variants that escape neutralising antibodies hampers the development of vaccines and therapeutic antibodies against SARS-CoV-2. IGHV3-53/3-66-derived public antibodies, which are generally specific to the prototype virus and are frequently induced in infected or vaccinated individuals, show minimal affinity maturation and high potency against prototype SARS-CoV-2. Monoclonal antibodies isolated from a Delta breakthrough infection case were analysed for cross-neutralising activities against SARS-CoV-2 variants. The broadly neutralising antibody K4-66 was further analysed in a hamster model, and the effect of somatic hypermutations was assessed using the inferred germline precursor. Antibodies derived from IGHV3-53/3-66 showed broader neutralising activity than antibodies derived from IGHV1-69 and other IGHV genes. IGHV3-53/3-66 antibodies neutralised the Delta variant better than the IGHV1-69 antibodies, suggesting that the IGHV3-53/3-66 antibodies were further maturated by Delta breakthrough infection. One IGHV3-53/3-66 antibody, K4-66, neutralised all Omicron subvariants tested, including EG.5.1, BA.2.86, and JN.1, and decreased the viral load in the lungs of hamsters infected with Omicron subvariant XBB.1.5. The importance of somatic hypermutations was demonstrated by the loss of neutralising activity of the inferred germline precursor of K4-66 against Beta and Omicron variants. Broadly neutralising IGHV3-53/3-66 antibodies have potential as a target for the development of effective vaccines and therapeutic antibodies against newly emerging SARS-CoV-2 variants. This work was supported by grants from AMED (JP23ym0126048, JP22ym0126048, JP21ym0126048, JP23wm0125002, JP233fa627001, JP223fa627009, JP24jf0126002, and JP22fk0108572), and the JSPS (JP21H02970, JK23K20041, and JPJSCCA20240006).


  • Organizational Affiliation
    • Collaborative Research Program with the Chemo-Sero-Therapeutic Research Institute for Anti-viral Agents and Hematological Diseases, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan. Electronic address: tkuwata@kumamoto-u.ac.jp.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
antigen-binding fragments (Fabs)
A, C
218Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
antigen-binding fragments (Fabs)
B, D
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.288 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 0.264 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.45α = 90
b = 147.45β = 90
c = 154.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
ADDREFdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references