3VW3

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

Summary for 3VW3

• Entry DOI: 10.2210/pdb3vw3/pdb
• Related: 1EHL 1KEG
• Descriptor: Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain), Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain), DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3'), ... (6 entities in total)
• Functional Keywords: protein-dna complex, dna (6-4) photoproduct, immunoglobulin, immune system-dna complex, immune system/dna
• Biological source: Mus musculus; More
• Total number of polymer chains: 4
• Total formula weight: 58903.42

Authors

Yokoyama, H.,Mizutani, R.,Satow, Y. (deposition date: 2012-07-30, release date: 2013-03-27, Last modification date: 2024-11-06)

Primary citation

Yokoyama, H.,Mizutani, R.,Satow, Y.
Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab
Acta Crystallogr.,Sect.D, 69:504-512, 2013

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)-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.

PubMed: 23519658
DOI: 10.1107/S0907444912050007

Experimental method

X-RAY DIFFRACTION (2.5 Å)