3x3c: Difference between revisions

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 ==Crystal structure of the light-driven sodium pump KR2 in neutral state==
-<StructureSection load='3x3c' size='340' side='right' caption='[[3x3c]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3x3c' size='340' side='right'caption='[[3x3c]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3x3c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3X3C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3x3c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dokdonia_eikasta Dokdonia eikasta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X3C FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3x3b|3x3b]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></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=3x3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x3c OCA], [http://pdbe.org/3x3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3x3c RCSB], [http://www.ebi.ac.uk/pdbsum/3x3c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3x3c ProSAT]</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=3x3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x3c OCA], [https://pdbe.org/3x3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x3c RCSB], [https://www.ebi.ac.uk/pdbsum/3x3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x3c ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/N0DKS8_9FLAO N0DKS8_9FLAO]
-Krokinobacter eikastus rhodopsin 2 (KR2) is the first light-driven Na(+) pump discovered, and is viewed as a potential next-generation optogenetics tool. Since the positively charged Schiff base proton, located within the ion-conducting pathway of all light-driven ion pumps, was thought to prohibit the transport of a non-proton cation, the discovery of KR2 raised the question of how it achieves Na(+) transport. Here we present crystal structures of KR2 under neutral and acidic conditions, which represent the resting and M-like intermediate states, respectively. Structural and spectroscopic analyses revealed the gating mechanism, whereby the flipping of Asp116 sequesters the Schiff base proton from the conducting pathway to facilitate Na(+) transport. Together with the structure-based engineering of the first light-driven K(+) pumps, electrophysiological assays in mammalian neurons and behavioural assays in a nematode, our studies reveal the molecular basis for light-driven non-proton cation pumps and thus provide a framework that may advance the development of next-generation optogenetics.
-Structural basis for Na(+) transport mechanism by a light-driven Na(+) pump.,Kato HE, Inoue K, Abe-Yoshizumi R, Kato Y, Ono H, Konno M, Hososhima S, Ishizuka T, Hoque MR, Kunitomo H, Ito J, Yoshizawa S, Yamashita K, Takemoto M, Nishizawa T, Taniguchi R, Kogure K, Maturana AD, Iino Y, Yawo H, Ishitani R, Kandori H, Nureki O Nature. 2015 May 7;521(7550):48-53. doi: 10.1038/nature14322. Epub 2015 Apr 6. PMID:25849775<ref>PMID:25849775</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3x3c" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Rhodopsin|Rhodopsin]]
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Abe-Yoshizumi, R]]
+[[Category: Dokdonia eikasta]]
-[[Category: Hoque, M R]]
+[[Category: Large Structures]]
-[[Category: Hososhima, S]]
+[[Category: Abe-Yoshizumi R]]
-[[Category: Iino, Y]]
+[[Category: Hoque MR]]
-[[Category: Inoue, K]]
+[[Category: Hososhima S]]
-[[Category: Ishitani, R]]
+[[Category: Iino Y]]
-[[Category: Ishizuka, T]]
+[[Category: Inoue K]]
-[[Category: Ito, J]]
+[[Category: Ishitani R]]
-[[Category: Kandori, H]]
+[[Category: Ishizuka T]]
-[[Category: Kato, H E]]
+[[Category: Ito J]]
-[[Category: Kato, Y]]
+[[Category: Kandori H]]
-[[Category: Kogure, K]]
+[[Category: Kato HE]]
-[[Category: Konno, M]]
+[[Category: Kato Y]]
-[[Category: Kunitomo, H]]
+[[Category: Kogure K]]
-[[Category: Maturana, A D]]
+[[Category: Konno M]]
-[[Category: Nishizawa, T]]
+[[Category: Kunitomo H]]
-[[Category: Nureki, O]]
+[[Category: Maturana AD]]
-[[Category: Ono, H]]
+[[Category: Nishizawa T]]
-[[Category: Takemoto, M]]
+[[Category: Nureki O]]
-[[Category: Taniguchi, R]]
+[[Category: Ono H]]
-[[Category: Yamashita, K]]
+[[Category: Takemoto M]]
-[[Category: Yawo, H]]
+[[Category: Taniguchi R]]
-[[Category: Yoshizawa, S]]
+[[Category: Yamashita K]]
-[[Category: Light-driven sodium pump]]
+[[Category: Yawo H]]
-[[Category: Membrane protein]]
+[[Category: Yoshizawa S]]