9YKA | pdb_00009yka

Cryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9YKA

This is version 1.1 of the entry. See complete history

Literature

Structure and immunogenicity of an engineered soluble prefusion-stabilized EBV gB antigen.

McCool, R.S.Acreman, C.M.Powell, A.E.Picucci, S.I.Stieh, D.J.Chou, C.W.Huynh, J.Caruso, H.Park, S.O'Rear, J.Chen, J.L.Palanski, B.A.Byrne, P.O.Sponholtz, M.R.Kim, J.Ledgerwood, J.E.Weidenbacher, P.A.McLellan, J.S.

(2026) Nat Commun 17: 1197-1197

  • DOI: https://doi.org/10.1038/s41467-025-67969-x
  • Primary Citation Related Structures: 
    9OAL, 9YKA

  • PubMed Abstract: 

    Epstein-Barr virus (EBV), the causative agent of mononucleosis, is linked to over 140,000 annual cancer-related deaths globally and increases the risk of multiple sclerosis by up to 32-fold. As a herpesvirus, EBV establishes lifelong infection, and over 90% of U.S. adults are EBV-seropositive. Despite its significant disease burden, no approved EBV vaccines or therapeutics exist. Among EBV envelope glycoproteins, the fusion protein (gB) is strictly required for epithelial and B cell infection. Here, using a combination of AlphaFold-guided modeling, rational design, and ThermoMPNN-informed optimization, we engineer a stabilized prefusion gB variant, C3-GT. This construct incorporates two inter-protomeric disulfide bonds and three cavity-filling substitutions, resulting in a melting temperature of 54 °C. Cryo-EM analysis of this construct reveals the prefusion structure of EBV gB, providing insights into the structural transitions required to adopt the postfusion conformation. Murine immunizations and depletion studies with human sera suggest a trend toward improved functional immunogenicity of C3-GT compared to postfusion gB. Collectively, these studies define engineering principles to stabilize class III fusion proteins, provide reagents to interrogate the human antibody response to EBV gB, and lay a foundation for further studies to develop EBV gB-based vaccine candidates.


  • Organizational Affiliation
    • Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 358.91 kDa 
  • Atom Count: 11,157 
  • Modeled Residue Count: 1,431 
  • Deposited Residue Count: 3,243 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AMMO2 fab heavy chainA [auth F],
C [auth H],
E [auth D]
133Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AMMO2 fab light chainB [auth G],
D [auth I],
F [auth E]
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
BALF4G [auth A],
H [auth B],
I [auth C]
734human gammaherpesvirus 4Mutation(s): 0 
Gene Names: BALF4
UniProt
Find proteins for P0C762 (Human herpesvirus 4 (strain GD1))
Explore P0C762 
Go to UniProtKB:  P0C762
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C762
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-31
    Type: Initial release
  • Version 1.1: 2026-07-15
    Changes: Data collection, Database references