6smq: Difference between revisions

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 ==Structure of the RagAB peptide importer in the 'open-closed' state==
-<StructureSection load='6smq' size='340' side='right'caption='[[6smq]]' scene=''>
+<StructureSection load='6smq' size='340' side='right'caption='[[6smq]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SMQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SMQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6smq]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Porgi Porgi] and [http://en.wikipedia.org/wiki/Porphyromonas_gingivalis_w83 Porphyromonas gingivalis w83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SMQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SMQ FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6smq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6smq OCA], [http://pdbe.org/6smq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6smq RCSB], [http://www.ebi.ac.uk/pdbsum/6smq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6smq ProSAT]</span></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PL:(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL+15-METHYLHEXADECANOATE'>5PL</scene>, <scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6sm3|6sm3]], [[6sml|6sml]], [[6sli|6sli]], [[6slj|6slj]], [[6sln|6sln]]</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6smq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6smq OCA], [http://pdbe.org/6smq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6smq RCSB], [http://www.ebi.ac.uk/pdbsum/6smq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6smq ProSAT]</span></td></tr>
 </table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagA2B2 complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a 'pedal bin' mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis.
+Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis.,Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Basle A, Ranson NA, Potempa J, van den Berg B Nat Microbiol. 2020 May 11. pii: 10.1038/s41564-020-0716-y. doi:, 10.1038/s41564-020-0716-y. PMID:32393857<ref>PMID:32393857</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6smq" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Ranson NA]]
+[[Category: Porgi]]
-[[Category: White JBR]]
+[[Category: Porphyromonas gingivalis w83]]
-[[Category: Van den Berg B]]
+[[Category: Berg, B van den]]
+[[Category: Ranson, N A]]
+[[Category: White, J B.R]]
+[[Category: Beta-barrel]]
+[[Category: Membrane protein]]
+[[Category: Omp]]
+[[Category: Tonb-dependent]]
+[[Category: Transporter]]