8KHR | pdb_00008khr

Cryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1

• PDB DOI: https://doi.org/10.2210/pdb8KHR/pdb
• EM Map EMD-37249: EMDB EMDataResource

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


• Deposited: 2023-08-22 Released: 2024-06-19 
• Deposition Author(s): Fang, X.Y., Zhao, G.X., Zeng, M.S., Liu, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Potent human monoclonal antibodies targeting Epstein-Barr virus gp42 reveal vulnerable sites for virus infection.

Zhao, G.X., Fang, X.Y., Bu, G.L., Chen, S.J., Sun, C., Li, T., Xie, C., Wang, Y., Li, S.X., Meng, N., Feng, G.K., Zhong, Q., Kong, X.W., Liu, Z., Zeng, M.S.

(2024) Cell Rep Med 5: 101573-101573

• PubMed: 38776874 
• DOI: https://doi.org/10.1016/j.xcrm.2024.101573
• Primary Citation Related Structures: 
  8KHR


• PubMed Abstract: 
  

  Epstein-Barr virus (EBV) is linked to various malignancies and autoimmune diseases, posing a significant global health challenge due to the lack of specific treatments or vaccines. Despite its crucial role in EBV infection in B cells, the mechanisms of the glycoprotein gp42 remain elusive. In this study, we construct an antibody phage library from 100 EBV-positive individuals, leading to the identification of two human monoclonal antibodies, 2B7 and 2C1. These antibodies effectively neutralize EBV infection in vitro and in vivo while preserving gp42's interaction with the human leukocyte antigen class II (HLA-II) receptor. Structural analysis unveils their distinct binding epitopes on gp42, different from the HLA-II binding site. Furthermore, both 2B7 and 2C1 demonstrate potent neutralization of EBV infection in HLA-II-positive epithelial cells, expanding our understanding of gp42's role. Overall, this study introduces two human anti-gp42 antibodies with potential implications for developing EBV vaccines targeting gp42 epitopes, addressing a critical gap in EBV research.

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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, Guangzhou 510060, China.
Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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, Guangzhou 510060, China; Department of Otorhinolaryngology, Sun Yat-sen Memorial Hospital, Guangzhou, China. Electronic address: [e-mail].
Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China. Electronic address: [e-mail].
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, Guangzhou 510060, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 130.59 kDa 
• Atom Count: 8,320 
• Modeled Residue Count: 1,138 
• Deposited Residue Count: 1,176 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble gp42	A [auth C]	196	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BZLF2
UniProt
Find proteins for P0C6Z5 (Epstein-Barr virus (strain GD1)) Explore P0C6Z5  Go to UniProtKB:  P0C6Z5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2C1 heavy chain	B [auth H]	111	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
2C1 light chain	C [auth L]	107	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein H	D [auth A]	655	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BXLF2, gH
UniProt
Find proteins for Q3KSQ3 (Epstein-Barr virus (strain GD1)) Explore Q3KSQ3  Go to UniProtKB:  Q3KSQ3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein L	E [auth B]	107	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BKRF2, gL
UniProt
Find proteins for Q3KSS3 (Epstein-Barr virus (strain GD1)) Explore Q3KSS3  Go to UniProtKB:  Q3KSS3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 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: 2024-06-19 
Deposition Author(s): Fang, X.Y., Zhao, G.X., Zeng, M.S., Liu, Z.

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Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary