6IDG | pdb_00006idg

antibody 64M-5 Fab in complex with dT(6-4)T

• PDB DOI: https://doi.org/10.2210/pdb6IDG/pdb
• NAKB: 6IDG

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, synthetic construct
• Mutation(s): No 


• Deposited: 2018-09-10 Released: 2019-02-13 
• Deposition Author(s): Yokoyama, H., Mizutani, R., Noguchi, S., Hayashida, N.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms.

Yokoyama, H., Mizutani, R., Noguchi, S., Hayashida, N.

(2019) Acta Crystallogr F Struct Biol Commun 75: 80-88

• PubMed: 30713158 
• DOI: https://doi.org/10.1107/S2053230X18017661
• Primary Citation Related Structures: 
  6IDG, 6IDH


• PubMed Abstract: 
  

  DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts produced by ultraviolet light are mutagenic and carcinogenic. The crystal structures of the anti-(6-4) photoproduct antibody 64M-5 Fab and of its complex with dT(6-4)T were determined at 2.5 and 2.0 Å resolution, respectively. A comparison between the dT(6-4)T-liganded and unliganded structures indicates that the side chain of His93L is greatly rotated and shifted on binding to dT(6-4)T, leading to the formation of an electrostatic interaction with the phosphate moiety of dT(6-4)T, which shows a remarkable induced fit. Based on a comparison of the dT(6-4)T-liganded structures of the 64M-5 and 64M-2 Fabs, the electrostatic interaction between the side chain of His93L in 64M-5 and the phosphate moiety of dT(6-4)T is lost for Leu93L in 64M-2, while Arg90L in 64M-5 instead of Gln90L in 64M-2 stabilizes the conformation of complementarity-determining region (CDR) L3. These differences contribute to the higher affinity of 64M-5 for dT(6-4)T compared with that of 64M-2.

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Organizational Affiliation: 
• Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
Graduate School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan.
Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.
Division of Molecular Gerontology and Anti-Ageing Medicine, Department of Biochemistry and Molecular Biology, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.39 kDa 
• Atom Count: 3,780 
• Modeled Residue Count: 440 
• Deposited Residue Count: 440 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)	A [auth L]	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)	B [auth H]	221	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(64T)P*(5PY))-3')	C [auth A]	2	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.62	α = 90
b = 100.865	β = 90
c = 51.666	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-13 
Deposition Author(s): Yokoyama, H., Mizutani, R., Noguchi, S., Hayashida, N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	17K07316

Revision History  

• Version 1.0: 2019-02-13
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary