9JE3 | pdb_00009je3

Structure of #2-911 Fab in complex with MEDI8852 Fab

• PDB DOI: https://doi.org/10.2210/pdb9JE3/pdb

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


• Deposited: 2024-09-02 Released: 2025-09-03 
• Deposition Author(s): Itou, H., Sano, K., Ainai, A., Suzuki, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.204 (DCC) 

Starting Models: experimental

Literature

Anti-idiotypic antibodies as molecular mimics of conserved influenza hemagglutinin epitopes.

Itou, H., Sano, K., Ainai, A., Otsuki, K., Inoue, T., Hemmi, T., Hasegawa, H., Suzuki, T.

(2026) Protein Sci 35: e70795-e70795

• PubMed: 42742346 
• DOI: https://doi.org/10.1002/pro.70795
• Primary Citation Related Structures: 
  9JE3


• PubMed Abstract: 
  

  Broadly neutralizing antibodies (bNAbs) provide insights for developing universal influenza vaccines through their ability to neutralize diverse viral strains. However, designing antigens that reliably elicit bNAb responses remains challenging due to the difficulty in targeting conserved epitopes with a single antigen. We developed a method using anti-idiotypic antibodies (IDs) to generate antigens that induce cross-reactive antibodies against diverse influenza A and B hemagglutinins. Our approach leverages IDs that mimic the conformational epitopes targeted by bNAbs. Structural analysis reveals conformational similarity between bNAb-ID and bNAb-HA-binding interfaces, providing mechanistic insight into molecular mimicry. These epitope-mimicking IDs function as effective immunogens, inducing highly cross-reactive antibodies. This study demonstrates the feasibility and structural basis of molecular mimicry-based antigen design for targeting conserved conformational epitopes. Although these findings establish proof of concept, vaccine applicability requires further investigation.

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Organizational Affiliation: 
• Chiome Bioscience Inc., Tokyo, Japan.
Influenza Research Center, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo, Japan.
Institute for Vaccine Research and Development, Hokkaido University, Hokkaido, Japan.
Department of Infections Disease Pathology, National Institute of Infectious Diseases, Japan Institute for Health Security, Tokyo, Japan.
Department of Virus Research, Kyoto University, Kyoto, Japan.
Department of Infectious Disease Pathobiology, Graduate School of Medicine, Chiba University, Chiba, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 189.05 kDa 
• Atom Count: 13,553 
• Modeled Residue Count: 1,739 
• Deposited Residue Count: 1,740 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
#2-911 Fab heavy chain	A [auth E], E [auth A]	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
#2-911 Fab light chain	B [auth F], F [auth B]	215	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MEDI8852 Fab heavy chain	C [auth G], G [auth C]	228	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MEDI8852 Fab light chain	D [auth H], H [auth D]	210	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	I [auth X], J [auth I], K [auth J]	2		N/A
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	L [auth H], M [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	I, J, K [auth X]	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.204 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.283	α = 90
b = 151.111	β = 90
c = 176.368	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Itou, H., Sano, K., Ainai, A., Suzuki, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release
  
• Version 1.1: 2026-09-23
  Changes: Database references