9LUY | pdb_00009luy

Single-chain Fv antibody of G2 fused with antigen peptide from chicken chromosome 6 C10orf76 homolog

• PDB DOI: https://doi.org/10.2210/pdb9LUY/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Gallus gallus, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-10 Released: 2025-06-11 
• Deposition Author(s): Hanazono, Y., Yabuno, S., Hayashi, T., Numoto, N., Ito, N., Oda, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structures reveal how the multispecific antibody G2 achieves binding to different peptides.

Hanazono, Y., Yabuno, S., Hayashi, T., Numoto, N., Kamatari, Y.O., Ito, N., Oda, M.

(2025) FEBS Lett 

• PubMed: 40527602 
• DOI: https://doi.org/10.1002/1873-3468.70095
• Primary Citation Related Structures: 
  9LUX, 9LUY


• PubMed Abstract: 
  

  Monoclonal antibody G2, obtained via immunization with the chicken prion protein (ChPrP), has unique antigen-binding specificity. G2 specifically binds to the ChPrP-derived peptide (Pep18mer) as expected, but also to three other peptides. In this study, we determined the crystal structures of G2 single-chain Fv antibodies covalently linked to Pep18mer and another peptide, PepH4P6. Both bound peptides formed similar U-shaped structures that stuck into the G2 antigen-binding pocket. Their three-dimensional structures were stabilized by interactions within the peptides, and the structure of the bound Pep18mer was similar to that of the corresponding ChPrP region. G2 acquired the binding ability to both Pep18mer and PepH4P6 via deletion of the 95th residue of the light chain during affinity maturation, consistent with our structural analysis.

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Organizational Affiliation: 
• Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, Japan.
Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Japan.
Life Science Research Center, Gifu University, Japan.
Institute for Glyco-Core Research (iGCORE), Gifu University, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.21 kDa 
• Atom Count: 2,100 
• Modeled Residue Count: 242 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-chain Fv antibody of G2 fused with antigen peptide from chicken chromosome 6 C10orf76 homolog	A	273	Gallus gallus, Mus musculus This entity is chimeric	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.054	α = 90
b = 71.39	β = 100.908
c = 43.352	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Hanazono, Y., Yabuno, S., Hayashi, T., Numoto, N., Ito, N., Oda, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Database references