6LCS | pdb_00006lcs

Crystal structure of 73MuL9 Fv-clasp fragment in complex with GA-pyridine analogue

• PDB DOI: https://doi.org/10.2210/pdb6LCS/pdb

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


• Deposited: 2019-11-19 Released: 2020-11-25 
• Deposition Author(s): Nakamura, T., Takagi, J., Yamagata, Y., Morioka, H.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Molecular recognition of a single-chain Fv antibody specific for GA-pyridine, an advanced glycation end-product (AGE), elucidated using biophysical techniques and synthetic antigen analogues.

Kobashigawa, Y., Ohara, T., Morita, K., Toyota, Y., Nakamura, T., Kotani, S., Arimori, T., Yamauchi, S., Liu, C., Kitazaki, M., Wakeyama-Miyazaki, Y., Suwa, Y., Uchida-Kamekura, M., Fukuda, N., Sato, T., Nakajima, M., Takagi, J., Yamagata, Y., Morioka, H.

(2021) J Biochem 170: 379-387

• PubMed: 34185078 
• DOI: https://doi.org/10.1093/jb/mvab056
• Primary Citation Related Structures: 
  6LCS


• PubMed Abstract: 
  

  Advanced glycation end-products (AGEs) are a heterogeneous group of compounds formed by non-enzymatic reaction between reducing-sugar and Arg/Lys in proteins and are involved in various diabetic complications. GA-pyridine is derived from glycolaldehyde and is one of the most cytotoxic AGEs. Here, we established a single-chain Fv (scFv) antibody against GA-pyridine, 73MuL9-scFv, and examined the details of its specificity and antigen recognition by using various techniques involving biophysics, chemical biology and structural biology. We also synthesized several compounds that differ slightly in regard to the position and number of GA-pyridine substituent groups, and revealed that GA-pyridine was specifically bound to 73MuL9-scFv. Thermodynamic analysis revealed that the association of GA-pyridine to 73MuL9-scFv was an exothermic and enthalpy driven reaction, and thus that the antigen recognition involved multiple specific interactions. Crystallographic analysis of the Fv fragment of 73MuL9-scFv revealed that several CH-π and hydrogen bond interactions took place between the Fv-fragment and GA-pyridine, which was consistent with the results of thermodynamic analysis. Further studies using 73MuL9-scFv as a tool to clarify the relevance of GA-pyridine to diabetic complications are warranted.

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Organizational Affiliation: 
• Department of Analytical and Biophysical Chemistry, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
Priority Organization for Innovation and Excellence, Kumamoto University, 2-39-1, Kurokami, Chuo-ku, Kumamoto 860-8555, Japan.
Department of Organic Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, 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: 38.67 kDa 
• Atom Count: 2,705 
• Modeled Residue Count: 329 
• Deposited Residue Count: 332 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VH-SARAH	A	171	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VL-SARAH	B	161	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E9R (Subject of Investigation/LOI)	C [auth A]	(2~{S})-6-[4-(hydroxymethyl)-3-oxidanyl-pyridin-1-ium-1-yl]-2-(phenylmethoxycarbonylamino)hexanoic acid C20 H25 N2 O6 MCKINXUETXTBTK-KRWDZBQOSA-O
PO4	D [auth A], E [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.260 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.15	α = 90
b = 91.15	β = 90
c = 119.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Nakamura, T., Takagi, J., Yamagata, Y., Morioka, H.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2021-12-08
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary