9IA3 | pdb_00009ia3

Bc8.108 Fab bound to preS2 peptide

• PDB DOI: https://doi.org/10.2210/pdb9IA3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Hepatitis B virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-02-07 Released: 2025-11-26 
• Deposition Author(s): Mechaly, A.E., Haouz, A., Beretta, M., Caillet-Saguy, C., Mouquet, H.
• Funding Organization(s): Pasteur Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: in silico

Literature

In vivo efficacy of combined human broadly neutralizing antibodies against hepatitis B virus.

Beretta, M., Mechaly, A., Planchais, C., Haouz, A., Caillet-Saguy, C., Szerman, N., Aronthippaitoon, Y., Ungeheuer, M.N., Pol, S., Gaudy-Graffin, C., Sureau, C., Bourgine, M., Mouquet, H.

(2025) Cell Rep 44: 116705-116705

• PubMed: 41405995 
• DOI: https://doi.org/10.1016/j.celrep.2025.116705
• Primary Citation Related Structures: 
  9IA3, 9IA4, 9IAT


• PubMed Abstract: 
  

  Antibodies targeting the hepatitis B virus (HBV) surface antigens (HBsAg) are essential for the prevention and control of HBV infection, yet their molecular and functional properties remain incompletely understood. Here, we characterize HBV seroconverter-derived human memory B cell monoclonal antibodies targeting preS1, preS2, and small (S) HBsAg regions. We find that broadly reactive anti-preS2 antibodies neutralize HBV and exert Fc-dependent effector functions that significantly contribute to their in vivo antiviral activity in HBV-carrier mice. Mapping and structural analysis reveal that they target an immunodominant epitope at the N terminus of preS2. Combining anti-preS2 and anti-S broadly neutralizing antibodies (bNAbs) isolated from the same donor profoundly and durably reduces antigenemia and viremia in HBV-carrier mice. These findings underscore the antiviral potential of anti-preS2 antibodies, particularly when combined with potent anti-S bNAbs, emphasizing their relevance for enhancing HBV vaccine efficacy and advancing immunotherapy development.

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Organizational Affiliation: 
• Institut Pasteur, Université Paris Cité, Humoral Immunology Unit, 75015 Paris, France.
Institut Pasteur, Université Paris Cité, Crystallography Platform-C2RT, 75015 Paris, France.
INSERM U1259, Université de Tours, 37044 Tours, France.
Institut Pasteur, ICAReB-Biobank, Centre de Ressources Biologiques, 75015 Paris, France.
AP-HP Centre, Université Paris Centre, Groupe Hospitalier Cochin Port Royal, DMU Cancérologie et spécialités médico-chirurgicales, Service des Maladies du foie, Université Paris Cité, 75006 Paris, France.
Laboratoire de Bactériologie-Virologie-Hygiène, CHRU de Tours, INSERM U1259, 37044 Tours, France.
Institut Pasteur, Université Paris Cité, Humoral Immunology Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, Department of Virology, 75015 Paris, France.
Institut Pasteur, Université Paris Cité, Humoral Immunology Unit, 75015 Paris, France. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.67 kDa 
• Atom Count: 4,321 
• Modeled Residue Count: 466 
• Deposited Residue Count: 466 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Bc8.108 light chain	A	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Bc8.108 heavy chain	B	228	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large S protein	C [auth E]	23	Hepatitis B virus	Mutation(s): 0
UniProt
Find proteins for B2Y6K4 (Hepatitis B virus) Explore B2Y6K4  Go to UniProtKB:  B2Y6K4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.198	α = 90
b = 65.131	β = 106.85
c = 100.635	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Mechaly, A.E., Haouz, A., Beretta, M., Caillet-Saguy, C., Mouquet, H.

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Funding Organization	Location	Grant Number
Pasteur Institute	France	--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2026-05-06
  Changes: Database references