8XS2 | pdb_00008xs2

Crystal structure of Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219 with addition of fluorophore TAMRA

• PDB DOI: https://doi.org/10.2210/pdb8XS2/pdb

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


• Deposited: 2024-01-08 Released: 2025-01-15 
• Deposition Author(s): Yazaki, S., Ueda, H., Arai, R.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.244 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Antigen-Binding Fragment of Anti-Osteocalcin Antibody KTM219.

Yazaki, S., Komatsu, M., Dong, J., Ueda, H., Arai, R.

(2025) Int J Mol Sci 26

• PubMed: 39859361 
• DOI: https://doi.org/10.3390/ijms26020648
• Primary Citation of Related Structures:  
  8XS1, 8XS2


• PubMed Abstract: 
  

  Osteocalcin is a useful biomarker for bone formation and bone-related diseases. KTM219 is an anti-osteocalcin C-terminal peptide antibody. The single-chain variable region (scFv) and antigen-binding fragment (Fab) of KTM219 are applicable to the Quenchbody (Q-body) immunoassay. Q-body is a new type of fluorescent immunosensor, which is scFv or Fab labeled with a fluorescent dye. When Q-body binds to its antigen, the fluorescence intensity increases. The highly sensitive detection of antigens by changes in fluorescence intensity is performed in a single step by mixing the sample and reagent. In this study, to reveal the recognition mechanism of the KTM219 antibody and to discuss the structural basis for Q-body, we solved the crystal structures of Fab of the anti-osteocalcin antibody KTM219 and its complex with the antigen osteocalcin C-terminal peptide (BGP-C7). Also, we solved the structure of a KTM219 Fab crystal grown in the presence of a fluorescent dye, carboxytetramethylrhodamine (TAMRA); however, tightly bound TAMRA was not found in the electron density map. We predicted the binding sites of TAMRA in the antigen-binding pocket by docking simulations. These results support the proposed Q-body mechanism. The crystal structures of KTM219 Fab would be useful for further development and improvement of Q-body fluorescent immunosensors.

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Organizational Affiliation: 
• Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Nagano, Japan.
Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan.
Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda 386-8567, Nagano, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.58 kDa 
• Atom Count: 3,505 
• Modeled Residue Count: 428 
• Deposited Residue Count: 481 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain fragment (Fd) of anti-osteocalcin antibody KTM219	A [auth H]	249	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of anti-osteocalcin antibody KTM219	B [auth L]	232	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth H], D [auth L]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.244 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.185	α = 90
b = 69.52	β = 90
c = 96.653	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Yazaki, S., Ueda, H., Arai, R.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H02522, JP17KK0104, JP16K05841, JP16H00761, JP24780097, JP15H04191, JP18H03851
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	Cooperative Research Program of Network Joint Research Center for Materials and Devices

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-02-05
  Changes: Database references