5ljv: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 5ljv is ON HOLD
+==MamK double helical filament==
+<SX load='5ljv' size='340' side='right' viewer='molstar' caption='[[5ljv]], [[Resolution|resolution]] 3.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5ljv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetospirillum_magneticum_AMB-1 Magnetospirillum magneticum AMB-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LJV FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.65&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5ljv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ljv OCA], [https://pdbe.org/5ljv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ljv RCSB], [https://www.ebi.ac.uk/pdbsum/5ljv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ljv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MAMK_MAGSA MAMK_MAGSA] Protein with ATPase activity which forms dynamic cytoplasmic filaments (probably with paralog MamK-like) that organize magnetosomes into long chains running parallel to the long axis of the cell (Probable) (PubMed:21883528, PubMed:28790202, PubMed:23204522, PubMed:24957623). Turnover of MamK filaments is probably promoted by MamK-like, which provides a monomer pool (PubMed:24957623). Forms twisted filaments in the presence of ATP or GTP (PubMed:20161777, PubMed:23204522, PubMed:27391173). Serves to close gaps between magnetosomes in the chain (PubMed:26884433). Interaction with MCP10 is involved in controlling the response to magnetic fields, possibly by controlling flagellar rotation (PubMed:20471399). Expression in E.coli yields a filament in the cell's longitudinal axis; the protein nucleates at several sites and one extremity of the filament is located at the cell pole (PubMed:17085581, PubMed:20161777).<ref>PMID:17085581</ref> <ref>PMID:20161777</ref> <ref>PMID:20471399</ref> <ref>PMID:21883528</ref> <ref>PMID:23204522</ref> <ref>PMID:24957623</ref> <ref>PMID:26884433</ref> <ref>PMID:27391173</ref> <ref>PMID:28790202</ref> <ref>PMID:16373532</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Magnetotactic bacteria produce iron-rich magnetic nanoparticles that are enclosed by membrane invaginations to form magnetosomes so they are able to sense and act upon Earth's magnetic field. In Magnetospirillum and other magnetotactic bacteria, to combine their magnetic moments, magnetosomes align along filaments formed by a bacterial actin homolog, MamK. Here, we present the crystal structure of a nonpolymerizing mutant of MamK from Magnetospirillum magneticum AMB-1 at 1.8-A resolution, revealing its close similarity to actin and MreB. The crystals contain AMPPNP-bound monomeric MamK in two different conformations. To investigate conformational changes associated with polymerization, we used unmodified MamK protein and cryo-EM with helical 3D reconstruction in RELION to obtain a density map and a fully refined atomic model of MamK in filamentous form at 3.6-A resolution. The filament is parallel (polar) double-helical, with a rise of 52.2 A and a twist of 23.8 degrees . As shown previously and unusually for actin-like filaments, the MamK subunits from each of the two strands are juxtaposed, creating an additional twofold axis along the filament. Compared with monomeric MamK, ADP-bound MamK in the filament undergoes a conformational change, rotating domains I and II against each other to further close the interdomain cleft between subdomains IB and IIB. The domain movement causes several loops to close around the nucleotide-binding pocket. Glu-143, a key residue for catalysis coordinating the magnesium ion, moves closer, presumably switching nucleotide hydrolysis upon polymerization-one of the hallmarks of cytomotive filaments of the actin type.
-Authors: Lowe, J.
+X-ray and cryo-EM structures of monomeric and filamentous actin-like protein MamK reveal changes associated with polymerization.,Lowe J, He S, Scheres SH, Savva CG Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):13396-13401. Epub 2016 Nov 7. PMID:27821762<ref>PMID:27821762</ref>
-Description: MamK double helical filament
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Lowe, J]]
+<div class="pdbe-citations 5ljv" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</SX>
+[[Category: Large Structures]]
+[[Category: Magnetospirillum magneticum AMB-1]]
+[[Category: Lowe J]]