8YY6 | pdb_00008yy6

Structure of a murine monoclonal antibody Fab5 targeting Epstein-Barr virus gB


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8YY6

This is version 1.1 of the entry. See complete history

Literature

Chimeric Glycoprotein Nanoparticles Elicit Robust Neutralizing Antibodies Against Epstein-Barr Virus.

Sun, C.Xie, C.Fang, X.Y.Hong, D.C.Zhang, H.Wu, P.H.Liu, Y.N.Bu, G.L.Cao, D.H.Si-Tu, M.Y.Peng, Y.J.Wang, J.Feng, G.K.Zhong, Q.Liu, Z.Zeng, M.S.

(2026) Adv Mater 38

  • DOI: https://doi.org/10.1002/adma.202507012
  • Primary Citation Related Structures: 
    8YY6

  • PubMed Abstract: 

    Epstein‒Barr virus (EBV) is a ubiquitous gammaherpesvirus linked to a broad spectrum of malignancies and autoimmune diseases with no approved therapeutic drugs or vaccines. EBV infection relies on the viral glycoproteins gB and gHgL, which, together, function as the fusion apparatus, mediating viral recognition and membrane fusion in both epithelial and B cells. Despite discovering potent neutralizing antibodies targeting gB and gHgL, the heterogeneous antigen structures and distribution of multiple glycoproteins in the virion hinder rational vaccine design targeting this apparatus complex. In this study, Chimeric nanoparticles (Chimeric-NPs) are designed that co-display EBV fusion apparatus and induce significantly more neutralizing antibodies in mice and nonhuman primates than the cocktail counterparts. It is further demonstrated that the Chimeric-NPs elicited neutralizing antibodies predominantly targeting gB, closely mimicking the antibody induction pattern by the whole EBV virion. Additionally, single-BCR sequencing is used to analyze the B cell response to Chimeric-NP, and a novel gB neutralizing antibody Fab5 targeting a new vulnerable site EBV gB is identified. These findings provide novel candidates and vaccine design strategies for EBV and reveal the underlying mechanisms of antibody induction and immune response regulation by chimera vaccines, with potential implications for all multi-antigen-harbored pathogens.


  • Organizational Affiliation
    • State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangdong, 510060, China.

Macromolecule Content 

  • Total Structure Weight: 368.69 kDa 
  • Atom Count: 18,183 
  • Modeled Residue Count: 2,334 
  • Deposited Residue Count: 3,312 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab5 H chainA [auth D],
D [auth E],
G
224Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab5 L chainB [auth F],
E [auth H],
H [auth I]
213Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
BALF4C [auth A],
F [auth B],
I [auth C]
667human gammaherpesvirus 4Mutation(s): 0 
Gene Names: BALF4
UniProt
Find proteins for R4R670 (Epstein-Barr virus (strain GD1))
Explore R4R670 
Go to UniProtKB:  R4R670
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4R670
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82030046

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2026-02-18
    Changes: Data collection, Database references