9UY9 | pdb_00009uy9

Macacine gammaherpesvirus 4 glycoprotein B in complex with Fab5

• PDB DOI: https://doi.org/10.2210/pdb9UY9/pdb
• EM Map EMD-64607: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Macacine gammaherpesvirus 4, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-05-15 Released: 2026-01-21 
• Deposition Author(s): Cheng, B.Z., Fang, X.Y., Xie, C., Sun, C., Liu, Z., Zeng, M.S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A broadly protective antibody targeting gammaherpesvirus gB.

Sun, C., Xie, C., Cheng, B.Z., Jiang, Z.Y., Wu, P.H., Fang, X.Y., Li, P.L., Tian, X.S., Zhou, H., Yang, Y.L., Wang, J., Sui, S.F., Liu, Z., Zeng, M.S.

(2026) Nature 653: 190-199

• PubMed: 41629701 
• DOI: https://doi.org/10.1038/s41586-026-10192-5
• Primary Citation Related Structures: 
  9UV4, 9UVC, 9UY9


• PubMed Abstract: 
  

  Gammaherpesvirus is a subfamily of herpesvirus, distinct phylogenetically from alphaherpesvirus and betaherpesvirus and characterized by its oncogenic subtypes, including Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus ¹ . It broadly infects humans and other vertebrates and causes various diseases and malignancies ^2,3 . However, no specific antiviral agents are available for each subtype or the whole family. gB is a common fusion protein that is vital for herpesvirus infection and is an ideal target for broad vaccine development; however, a lack of structural and mechanistic understanding of gB hinders this effort ⁴ . Here we report the molecular basis of broad gB binding and cross-genus virus neutralization by an antibody, Fab5. This antibody confers effective protection against authentic virus challenges in immunocompetent mice, non-human primates and humanized mice with murine, rhesus and human gammaherpesvirus. Cryo-electron microscopy structures reveal that Fab5 targets a conserved and vulnerable epitope of gammaherpesvirus gB that is antigenically exposed in both pre-fusion and post-fusion states. This finding not only demonstrates that Fab5 is a cross-genus antibody that is broadly reactive to gammaherpesvirus infection and pathogenesis progression, but also offers insights into potential common mechanisms for herpesvirus infection and facilitates the development of broad-spectrum vaccines against gammaherpesviruses.

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Organizational Affiliation: 
• State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China. [e-mail].
State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China.
Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, China. [e-mail].
Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China. [e-mail].
State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 376.54 kDa 
• Atom Count: 16,151 
• Modeled Residue Count: 2,310 
• Deposited Residue Count: 3,393 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macacine gammaherpesvirus 4 glycoprotein B	A, B, C	694	Macacine gammaherpesvirus 4	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab5 H chain	D [auth H], E [auth I], F [auth J]	224	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab5 L chain	G [auth L], H [auth M], I [auth N]	213	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Cheng, B.Z., Fang, X.Y., Xie, C., Sun, C., Liu, Z., Zeng, M.S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82030046

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release
  
• Version 1.1: 2026-02-18
  Changes: Data collection, Database references
• Version 1.2: 2026-04-08
  Changes: Data collection, Structure summary
• Version 1.3: 2026-05-20
  Changes: Data collection, Database references