This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
6idh
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==Antibody 64M-5 Fab in ligand-free form== | |
| + | <StructureSection load='6idh' size='340' side='right' caption='[[6idh]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6idh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IDH FirstGlance]. <br> | ||
| + | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6idh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idh OCA], [http://pdbe.org/6idh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6idh RCSB], [http://www.ebi.ac.uk/pdbsum/6idh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6idh ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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 A 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 degrees . 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. | ||
| - | + | Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab.,Yokoyama H, Mizutani R, Satow Y Acta Crystallogr D Biol Crystallogr. 2013 Apr;69(Pt 4):504-12. doi:, 10.1107/S0907444912050007. Epub 2013 Mar 9. PMID:23519658<ref>PMID:23519658</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 6idh" style="background-color:#fffaf0;"></div> | |
| - | [[Category: | + | == References == |
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Mus musculus]] | ||
[[Category: Hayashida, N]] | [[Category: Hayashida, N]] | ||
| + | [[Category: Mizutani, R]] | ||
[[Category: Noguchi, S]] | [[Category: Noguchi, S]] | ||
| + | [[Category: Yokoyama, H]] | ||
| + | [[Category: Fab]] | ||
| + | [[Category: Immune system]] | ||
| + | [[Category: Immunoglobulin]] | ||
Revision as of 09:32, 13 February 2019
Antibody 64M-5 Fab in ligand-free form
| |||||||||||
