9ISF | pdb_00009isf

Crystal structure of nanobody 14 in complex with HSV-2 gD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free: 
    0.347 (Depositor), 0.348 (DCC) 
  • R-Value Work: 
    0.301 (Depositor), 0.301 (DCC) 
  • R-Value Observed: 
    0.303 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

A potent protective bispecific nanobody targeting Herpes simplex virus gD reveals vulnerable epitope for neutralizing.

Hu, J.Tan, H.Wang, M.Deng, S.Liu, M.Zheng, P.Wang, A.Guo, M.Wang, J.Li, J.Qiu, H.Yao, C.Zhu, Z.Hasi, C.Pan, D.He, H.Huang, C.Shang, Y.Zhu, S.Jin, T.

(2025) Nat Commun 16: 4196-4196

  • DOI: https://doi.org/10.1038/s41467-025-58669-7
  • Primary Citation of Related Structures:  
    9ISF, 9ISH

  • PubMed Abstract: 

    Herpes simplex virus (HSV) causes significant health burden worldwide. Currently used antiviral drugs are effective but resistance can occur. Here, we report two high-affinity neutralizing nanobodies, namely Nb14 and Nb32, that target non-overlapping epitopes in HSV gD. Nb14 binds a neutralization epitope located in the N-A' interloop, which prevents the interaction between gD and gH/gL during the second step of conformational changes during membrane fusion after virus attachment. The bispecific nanobody dimer (Nb14-32-Fc) exhibits high potency in vitro and in vivo. Mechanistically, Nb14-32-Fc neutralizes HSVs at both the pre-and post-attachment stages and prevents cell-to-cell spread in vitro. Administration of Nb14-32-Fc at low dosage of 1 mg/kg provides 100% protection in an HSV-1 infection male mouse model and an HSV-2 infection female mouse model. Our results demonstrate that Nb14-32-Fc could serve as a promising drug candidate for treatment of HSV infection, especially in the cases of antiviral drug resistance and severe herpes encephalitis.


  • Organizational Affiliation

    Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, Anhui, 230001, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoprotein D275Human alphaherpesvirus 2Mutation(s): 0 
Gene Names: US6
UniProt
Find proteins for A0A1W6QD44 (Human herpesvirus 2)
Explore A0A1W6QD44 
Go to UniProtKB:  A0A1W6QD44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W6QD44
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 14129Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.72 Å
  • R-Value Free:  0.347 (Depositor), 0.348 (DCC) 
  • R-Value Work:  0.301 (Depositor), 0.301 (DCC) 
  • R-Value Observed: 0.303 (Depositor) 
Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.605α = 90
b = 107.605β = 90
c = 129.973γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82272301

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release