6idg

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==antibody 64M-5 Fab in complex with dT(6-4)T==
==antibody 64M-5 Fab in complex with dT(6-4)T==
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<StructureSection load='6idg' size='340' side='right' caption='[[6idg]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='6idg' size='340' side='right'caption='[[6idg]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6idg]] is a 3 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=6IDG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IDG FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6idg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IDG FirstGlance]. <br>
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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></td></tr>
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</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&#8491;</td></tr>
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<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=6idg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idg OCA], [http://pdbe.org/6idg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6idg RCSB], [http://www.ebi.ac.uk/pdbsum/6idg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6idg ProSAT]</span></td></tr>
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<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></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6idg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idg OCA], [https://pdbe.org/6idg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6idg RCSB], [https://www.ebi.ac.uk/pdbsum/6idg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6idg ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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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.
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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 A 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.
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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>
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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 Acta Crystallogr F Struct Biol Commun. 2019 Feb 1;75(Pt 2):80-88. doi:, 10.1107/S2053230X18017661. Epub 2019 Jan 23. PMID:30713158<ref>PMID:30713158</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 6idg" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 6idg" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Antibody 3D structures|Antibody 3D structures]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Hayashida, N]]
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[[Category: Synthetic construct]]
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[[Category: Mizutani, R]]
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[[Category: Hayashida N]]
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[[Category: Noguchi, S]]
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[[Category: Mizutani R]]
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[[Category: Yokoyama, H]]
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[[Category: Noguchi S]]
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[[Category: Fab]]
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[[Category: Yokoyama H]]
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[[Category: Immune system]]
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[[Category: Immunoglobulin]]
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Current revision

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

PDB ID 6idg

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