3vw3
From Proteopedia
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| - | {{STRUCTURE_3vw3| PDB=3vw3 | SCENE= }} | ||
| - | ===Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct=== | ||
| - | {{ABSTRACT_PUBMED_22349224}} | ||
| - | == | + | ==Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct== |
| - | [[3vw3]] is a 4 chain structure with sequence from [ | + | <StructureSection load='3vw3' size='340' side='right'caption='[[3vw3]], [[Resolution|resolution]] 2.50Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3vw3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VW3 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PY:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE'>5PY</scene>, <scene name='pdbligand=64T:5-HYDROXY-THYMIDINE-5-MONOPHOSPHATE'>64T</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vw3 OCA], [https://pdbe.org/3vw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vw3 RCSB], [https://www.ebi.ac.uk/pdbsum/3vw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vw3 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> | |
| - | <ref | + | |
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3vw3" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
| - | [[Category: Mizutani | + | [[Category: Mizutani R]] |
| - | [[Category: Satow | + | [[Category: Satow Y]] |
| - | [[Category: Yokoyama | + | [[Category: Yokoyama H]] |
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Current revision
Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct
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