3VW3

Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.,Sect.D 69: 504-512

  • DOI: 10.1107/S0907444912050007
  • Also Cited By: 6IDH, 6IDG

  • PubMed Abstract: 
  • DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by ultraviolet radiation have been implicated in mutagenesis and cancer. The crystal structure of double-stranded DNA containing the (6-4) photoproduct in complex with the anti-(6-4)-p ...

    DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by ultraviolet radiation have been implicated in mutagenesis and cancer. The crystal structure of double-stranded DNA containing the (6-4) photoproduct in complex with the anti-(6-4)-photoproduct antibody 64M-5 Fab was determined at 2.5 Å resolution. The T(6-4)T segment and the 5'-side adjacent adenosine are flipped out of the duplex and are accommodated in the concave antigen-binding pocket composed of six complementarity-determining regions (CDRs). A loop comprised of CDR L1 residues is inserted between the flipped-out T(6-4)T segment and the complementary DNA. The separation of strands by the insertion of the loop facilitates extensive and specific recognition of the photoproduct. The DNA helices flanking the T(6-4)T segment are kinked by 87°. The 64M-5 Fab recognizes the T(6-4)T segment dissociated from the complementary strand, indicating that the (6-4) photoproduct can be detected in double-stranded DNA as well as in single-stranded DNA using the 64M-5 antibody. The structure and recognition mode of the 64M-5 antibody were compared with those of the DNA (6-4) photolyase and nucleotide-excision repair protein DDB1-DDB2. These proteins have distinctive binding-site structures that are appropriate for their functions, and the flipping out of the photolesion and the kinking of the DNA are common to mutagenic (6-4) photoproducts recognized by proteins.


    Related Citations: 
    • Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides
      Yokoyama, H.,Mizutani, R.,Satow, Y.,Sato, K.,Komatsu, Y.,Ohtsuka, E.,Nikaido, O.
      (2012) Acta Crystallogr.,Sect.D 68: 232
    • 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

    School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan. h-yokoya@u-shizuoka-ken.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)
L
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)
H
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3')A18N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3')B18N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
H
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
64T
Query on 64T
A
DNA LINKINGC10 H17 N2 O9 PDT
5PY
Query on 5PY
A
DNA LINKINGC10 H15 N2 O7 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.430α = 90.00
b = 68.430β = 90.00
c = 243.658γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2014-04-30
    Type: Database references