6IDG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1107/S2053230X18017661
  • Primary Citation of Related Structures:  
    6IDH, 6IDG

  • 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 ...

    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.


    Related Citations: 
    • Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab
      Yokoyama, H., Mizutani, R., Satow, Y.
      (2013) Acta Crystallogr D Biol Crystallogr 69: 504
    • Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation
      Yokoyama, H., Mizutani, R., Satow, Y., Komatsu, Y., Ohtsuka, E., Nikaido, O.
      (2000) J Mol Biol 299: 711

    Organizational Affiliation

    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.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)L217Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)H221Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*(64T)P*(5PY))-3')A2synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.240 
    • R-Value Work: 0.192 
    • R-Value Observed: 0.192 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 84.62α = 90
    b = 100.865β = 90
    c = 51.666γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    X-PLORphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Japan Society for the Promotion of ScienceJapan17K07316

    Revision History 

    • Version 1.0: 2019-02-13
      Type: Initial release
    • Version 1.1: 2019-11-20
      Changes: Database references