8ZYF | pdb_00008zyf

Crystal structure of ZW2G10 Fab in complex with omicron RBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.285 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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Literature

Nasal delivery of secretory IgA confers enhanced neutralizing activity against Omicron variants compared to its IgG counterpart.

Zhang, G.Huang, P.Yuan, H.Li, E.Chi, X.Sun, H.Han, J.Fang, T.Dong, Y.Li, J.Wang, Y.Li, J.Chiu, S.Yu, C.

(2025) Mol Ther 33: 1687-1700

  • DOI: https://doi.org/10.1016/j.ymthe.2025.02.041
  • Primary Citation of Related Structures:  
    8ZYF

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its multiple variants continue to spread worldwide, causing respiratory symptoms primarily through mucosal infection. The mucosa serves as the primary barrier against viral entry, in which secretory immunoglobulin A (sIgA) plays a critical role in preventing infection. Here, we engineered and characterized a neutralizing monoclonal antibody, ZW2G10, in IgG, monomeric, dimeric, secretory IgA1, and IgA2 formats. All seven forms of the ZW2G10 antibody showed similar thermal stability. sIgA, especially sIgA1, displayed enhanced neutralizing activity against Omicron-lineage BA.2.75, BA.2.76 and BA.4/5 pseudoviruses compared to IgG. Nasal administration of sIgA1 conferred robust protection against the BA.2.76 pseudovirus in ACE2 transgenic mice, and its protective efficacy was superior to that of IgG. The crystal structure of Omicron receptor binding domain (RBD) and ZW2G10 antibody fragment (Fab) complex revealed that ZW2G10 had no clashes with ACE2. Thus, nasal administration of sIgA may serve as a promising tool for the prevention and treatment of Omicron infection.


  • Organizational Affiliation

    Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1A,
D [auth B]
195Severe acute respiratory syndrome coronavirus 2Mutation(s): 15 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ZW2G10 fab light chainB [auth D],
E [auth C]
214Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ZW2G10 fab heavy chainC [auth H],
F [auth E]
229Homo 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: 2.60 Å
  • R-Value Free:  0.285 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.664α = 90
b = 103.529β = 90
c = 299.352γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references