View source for 6dbi


==Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates==
<StructureSection load='6dbi' size='340' side='right' caption='[[6dbi]], [[Resolution|resolution]] 3.36&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6dbi]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6dbj|6dbj]], [[6dbl|6dbl]], [[6dbo|6dbo]], [[6dbq|6dbq]], [[6dbr|6dbr]], [[6dbu|6dbu]], [[6dbv|6dbv]], [[6dbw|6dbw]], [[6dbx|6dbx]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rag1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), rag2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </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=6dbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbi OCA], [http://pdbe.org/6dbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbi RCSB], [http://www.ebi.ac.uk/pdbsum/6dbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbi ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/MALE_ECOLI MALE_ECOLI]] Involved in the high-affinity maltose membrane transport system MalEFGK. Initial receptor for the active transport of and chemotaxis toward maltooligosaccharides. 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The mechanism for initiating DNA cleavage by DDE-family enzymes, including the RAG endonuclease, which initiates V(D)J recombination, is not well understood. Here we report six cryo-EM structures of zebrafish RAG in complex with one or two intact recombination signal sequences (RSSs), at up to 3.9-A resolution. Unexpectedly, these structures reveal DNA melting at the heptamer of the RSSs, thus resulting in a corkscrew-like rotation of coding-flank DNA and the positioning of the scissile phosphate in the active site. Substrate binding is associated with dimer opening and a piston-like movement in RAG1, first outward to accommodate unmelted DNA and then inward to wedge melted DNA. These precleavage complexes show limited base-specific contacts of RAG at the conserved terminal CAC/GTG sequence of the heptamer, thus suggesting conservation based on a propensity to unwind. CA and TG overwhelmingly dominate terminal sequences in transposons and retrotransposons, thereby implicating a universal mechanism for DNA melting during the initiation of retroviral integration and DNA transposition.

DNA melting initiates the RAG catalytic pathway.,Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H Nat Struct Mol Biol. 2018 Aug;25(8):732-742. doi: 10.1038/s41594-018-0098-5. Epub, 2018 Jul 30. PMID:30061602<ref>PMID:30061602</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6dbi" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Brachidanio rerio]]
[[Category: RING-type E3 ubiquitin transferase]]
[[Category: Liao, M]]
[[Category: Mi, W]]
[[Category: Ru, H]]
[[Category: Wu, H]]
[[Category: Nicked rss intermediate]]
[[Category: Paired complex]]
[[Category: Recombination-dna complex]]
[[Category: Synaptic rag complex]]