9LLD | pdb_00009lld

Post-fusion ectodomain of KSHV gB in complex with 2C4 Fab

• PDB DOI: https://doi.org/10.2210/pdb9LLD/pdb
• EM Map EMD-63198: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human gammaherpesvirus 8, Homo sapiens
• Expression System: Human gammaherpesvirus 8, Homo sapiens
• Mutation(s): No 


• Deposited: 2025-01-17 Released: 2025-03-05 
• Deposition Author(s): Fang, X.Y., Sun, C., Xie, C., Zeng, M.S., Liu, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and Antigenicity of Kaposi's Sarcoma-Associated Herpesvirus Glycoprotein B.

Fang, X.Y., Sun, C., Xie, C., Cheng, B.Z., Lu, Z.Z., Zhao, G.X., Sui, S.F., Zeng, M.S., Liu, Z.

(2025) Adv Sci (Weinh) 12: e2502231-e2502231

• PubMed: 40285648 
• DOI: https://doi.org/10.1002/advs.202502231
• Primary Citation of Related Structures:  
  8Y48, 9LLD


• PubMed Abstract: 
  

  Kaposi's sarcoma-associated herpesvirus (KSHV), a member of the human γ-herpesviruses family, exhibits extensive cellular tropism and is associated with Kaposi's sarcoma and various B-cell malignancies. Despite its clinical significance, no effective prophylactic vaccines or specific therapeutics are currently available to prevent or treat KSHV infection. Similar to other herpesviruses, KSHV depends on the envelope glycoprotein B (gB) for host receptor recognition and membrane fusion initiation, making gB a prime target for antiviral antibody or vaccine development. In this study, the high-resolution cryo-electron microscopy (cryo-EM) structure of KSHV gB is presented, revealing a unique trimeric conformation resembling the postfusion state observed in other herpesviruses. Additionally, the structure of the non-neutralizing monoclonal antibody 2C4 bound to KSHV gB domain IV is resolved. The comparative sequence and structure analyses reveal significant homology in neutralizing epitopes between KSHV and Epstein-Barr virus (EBV) gB, indicating a potential pathway for the development of broad-spectrum antiviral strategies. These findings provide a foundation for a deeper understanding of KSHV's infectious mechanism and pave the way for the creation of universal interventions against the human γ-herpesviruses.

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Organizational Affiliation: 
• Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
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, 510060, P. R. China.
Department of Dermatology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.

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: 374.54 kDa 
• Atom Count: 16,287 
• Modeled Residue Count: 2,334 
• Deposited Residue Count: 3,444 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Core gene UL27 family protein	A [auth C], D [auth A], G [auth B]	661	Human gammaherpesvirus 8	Mutation(s): 0  Gene Names: ORF8
UniProt
Find proteins for F5HB81 (Human herpesvirus 8 type P (isolate GK18)) Explore F5HB81  Go to UniProtKB:  F5HB81

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2C4 Fab H chain	B [auth H], E [auth D], H [auth E]	252	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
2C4 Fab L chain	C [auth L], F, I [auth G]	235	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Fang, X.Y., Sun, C., Xie, C., Zeng, M.S., Liu, Z.

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

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release
  
• Version 1.1: 2025-09-17
  Changes: Data collection, Database references