4xvl: Difference between revisions

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 ==Binary complex of human polymerase nu and DNA with the finger domain open==
-<StructureSection load='4xvl' size='340' side='right' caption='[[4xvl]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+<StructureSection load='4xvl' size='340' side='right'caption='[[4xvl]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xvl]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XVL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xvl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XVL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.301&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xvi|4xvi]], [[4xvk|4xvk]], [[4xvm|4xvm]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></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=4xvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvl OCA], [https://pdbe.org/4xvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xvl RCSB], [https://www.ebi.ac.uk/pdbsum/4xvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xvl ProSAT]</span></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=4xvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xvl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xvl RCSB], [http://www.ebi.ac.uk/pdbsum/4xvl PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/DPOLN_HUMAN DPOLN_HUMAN]
-All DNA replicases achieve high fidelity by a conserved mechanism, but each translesion polymerase carries out mutagenic DNA synthesis in its own way. Here we report crystal structures of human DNA polymerase nu (Pol nu), which is homologous to high-fidelity replicases yet is error prone. Instead of a simple open-to-closed movement of the O helix upon binding of a correct incoming nucleotide, Pol nu has a different open state and requires the finger domain to swing sideways and undergo both opening and closing motions to accommodate the nascent base pair. A single-amino acid substitution in the O helix of the finger domain improves the fidelity of Pol nu nearly ten-fold. A unique cavity and the flexibility of the thumb domain allow Pol nu to generate and accommodate a looped-out primer strand. Primer loop-out may be a mechanism for DNA trinucloetide-repeat expansion.
-How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis.,Lee YS, Gao Y, Yang W Nat Struct Mol Biol. 2015 Mar 16. doi: 10.1038/nsmb.2985. PMID:25775266<ref>PMID:25775266</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Homo sapiens]]
-[[Category: Lee, Y S]]
+[[Category: Large Structures]]
-[[Category: Yang, W]]
+[[Category: Lee Y-S]]
-[[Category: Error-prone dna synthesis]]
+[[Category: Yang W]]
-[[Category: Pol nu]]
-[[Category: Polymerase]]
-[[Category: Transferase-dna complex]]