8TNT | pdb_00008tnt

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2

• PDB DOI: https://doi.org/10.2210/pdb8TNT/pdb

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


• Deposited: 2023-08-02 Released: 2024-03-27 
• Deposition Author(s): Bu, W., Kumar, A., Board, N., Kim, J., Dowdell, K., Zhang, S., Lei, Y., Hostal, A., Krogmann, T., Wang, Y., Pittaluga, S., Marcotrigiano, J., Cohen, J.I.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.287 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Models: experimental

Literature

Epstein-Barr virus gp42 antibodies reveal sites of vulnerability for receptor binding and fusion to B cells.

Bu, W., Kumar, A., Board, N.L., Kim, J., Dowdell, K., Zhang, S., Lei, Y., Hostal, A., Krogmann, T., Wang, Y., Pittaluga, S., Marcotrigiano, J., Cohen, J.I.

(2024) Immunity 57: 559-573.e6

• PubMed: 38479361 
• DOI: https://doi.org/10.1016/j.immuni.2024.02.008
• Primary Citation Related Structures: 
  8TNN, 8TNT, 8TOO


• PubMed Abstract: 
  

  Epstein-Barr virus (EBV) causes infectious mononucleosis and is associated with B cell lymphomas. EBV glycoprotein 42 (gp42) binds HLA class II and activates membrane fusion with B cells. We isolated gp42-specific monoclonal antibodies (mAbs), A10 and 4C12, which use distinct mechanisms to neutralize virus infection. mAb A10 was more potent than the only known neutralizing gp42 mAb, F-2-1, in neutralizing EBV infection and blocking binding to HLA class II. mAb 4C12 was similar to mAb A10 in inhibiting glycoprotein-mediated B cell fusion but did not block receptor binding, and it was less effective in neutralizing infection. Crystallographic structures of gH/gL/gp42/A10 and gp42/4C12 complexes revealed two distinct sites of vulnerability on gp42 for receptor binding and B cell fusion. Passive transfer of mAb A10 into humanized mice conferred nearly 100% protection from viremia and EBV lymphomas after EBV challenge. These findings identify vulnerable sites on EBV that may facilitate therapeutics and vaccines.

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Organizational Affiliation: 
• Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Clinical Services Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].
Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A2B2C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 203.23 kDa 
• Atom Count: 13,731 
• Modeled Residue Count: 1,810 
• Deposited Residue Count: 1,855 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein H	A	656	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: gH
UniProt
Find proteins for P03231 (Epstein-Barr virus (strain B95-8)) Explore P03231  Go to UniProtKB:  P03231
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein L	B	112	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: gL
UniProt
Find proteins for P03212 (Epstein-Barr virus (strain B95-8)) Explore P03212  Go to UniProtKB:  P03212
Glycosylation
Glycosylation Sites: 1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein 42	C	191	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: BZLF2
UniProt
Find proteins for P03205 (Epstein-Barr virus (strain B95-8)) Explore P03205  Go to UniProtKB:  P03205

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
769C2 light chain	D	216	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
769C2 heavy chain	E	232	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
F-2-1 light chain	F	218	Mus musculus	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
F-2-1 heavy chain	G	230	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	H [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.287 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.317	α = 90
b = 85.172	β = 105.09
c = 119.714	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Bu, W., Kumar, A., Board, N., Kim, J., Dowdell, K., Zhang, S., Lei, Y., Hostal, A., Krogmann, T., Wang, Y., Pittaluga, S., Marcotrigiano, J., Cohen, J.I.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary