8IB1 | pdb_00008ib1

Structure of the LAH31 Fab bound to an influenza virus HA epitope peptide

• PDB DOI: https://doi.org/10.2210/pdb8IB1/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens, Influenza A virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-02-09 Released: 2023-07-26 
• Deposition Author(s): Suzuki, T., Hashiguchi, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Models: experimental

Literature

Structural basis for cross-group recognition of an influenza virus hemagglutinin antibody that targets postfusion stabilized epitope.

Tonouchi, K., Adachi, Y., Suzuki, T., Kuroda, D., Nishiyama, A., Yumoto, K., Takeyama, H., Suzuki, T., Hashiguchi, T., Takahashi, Y.

(2023) PLoS Pathog 19: e1011554-e1011554

• PubMed: 37556494 
• DOI: https://doi.org/10.1371/journal.ppat.1011554
• Primary Citation Related Structures: 
  8IB1


• PubMed Abstract: 
  

  Plasticity of influenza virus hemagglutinin (HA) conformation increases an opportunity to generate conserved non-native epitopes with unknown functionality. Here, we have performed an in-depth analysis of human monoclonal antibodies against a stem-helix region that is occluded in native prefusion yet exposed in postfusion HA. A stem-helix antibody, LAH31, provided IgG Fc-dependent cross-group protection by targeting a stem-helix kinked loop epitope, with a unique structure emerging in the postfusion state. The structural analysis and molecular modeling revealed key contact sites responsible for the epitope specificity and cross-group breadth that relies on somatically mutated light chain. LAH31 was inaccessible to the native prefusion HA expressed on cell surface; however, it bound to the HA structure present on infected cells with functional linkage to the Fc-mediated clearance. Our study uncovers a novel non-native epitope that emerges in the postfusion HA state, highlighting the utility of this epitope for a broadly protective antigen design.

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Organizational Affiliation: 
• Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan.
Department of Life Science and Medical Bioscience, Waseda University, Shinjuku, Tokyo, Japan.
Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics research, National Institutes of Biomedical Innovation, Health and Nutrition; Saito-Asagi, Ibaraki City, Osaka, Japan.
Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Shinjuku, Tokyo, Japan.
Research Organization for Nano and Life Innovation, Waseda University, Shinjuku, Tokyo, Japan.
Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan.
Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 56.89 kDa 
• Atom Count: 3,677 
• Modeled Residue Count: 447 
• Deposited Residue Count: 531 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LAH31 Fab light chain	A	245	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LAH31 Fab heavy chain	B	271	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	C	15	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7  Go to UniProtKB:  Q91MA7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.05	α = 90
b = 86.51	β = 90
c = 89.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Suzuki, T., Hashiguchi, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	223fa627009h0001

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Data collection, Database references
• Version 1.2: 2024-10-16
  Changes: Structure summary