3iyf: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 ==Atomic Model of the Lidless Mm-cpn in the Open State==
-<StructureSection load='3iyf' size='340' side='right' caption='[[3iyf]], [[Resolution|resolution]] 8.00&Aring;' scene=''>
+<SX load='3iyf' size='340' side='right' viewer='molstar' caption='[[3iyf]], [[Resolution|resolution]] 8.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3iye|3iye]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 Methanococcus maripaludis])</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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [https://pdbe.org/3iyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [https://www.ebi.ac.uk/pdbsum/3iyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyf 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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [http://www.ebi.ac.uk/pdbsum/3iyf PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q877G8_METMI Q877G8_METMI]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/3iyf_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/3iyf_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iyf ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.
-Mechanism of folding chamber closure in a group II chaperonin.,Zhang J, Baker ML, Schroder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W Nature. 2010 Jan 21;463(7279):379-83. PMID:20090755<ref>PMID:20090755</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Chaperonin|Chaperonin]]
+*[[Chaperonin 3D structures|Chaperonin 3D structures]]
-*[[Heat Shock Proteins|Heat Shock Proteins]]
+*[[Heat Shock Protein structures|Heat Shock Protein structures]]
-== References ==
-<references/>
 __TOC__
-</StructureSection>
+</SX>
+[[Category: Large Structures]]
 [[Category: Methanococcus maripaludis]]
-[[Category: Baker, M L]]
+[[Category: Baker ML]]
-[[Category: Chiu, W]]
+[[Category: Chiu W]]
-[[Category: Dougherty, M]]
+[[Category: Dougherty M]]
-[[Category: Douglas, N R]]
+[[Category: Douglas NR]]
-[[Category: Frydman, J]]
+[[Category: Frydman J]]
-[[Category: Fu, C J]]
+[[Category: Fu CJ]]
-[[Category: Jakana, J]]
+[[Category: Jakana J]]
-[[Category: Levitt, M]]
+[[Category: Levitt M]]
-[[Category: Ludtke, S J]]
+[[Category: Ludtke SJ]]
-[[Category: Reissmann, S]]
+[[Category: Reissmann S]]
-[[Category: Schroeder, G]]
+[[Category: Schroeder G]]
-[[Category: Zhang, J]]
+[[Category: Zhang J]]
-[[Category: Atp-binding]]
-[[Category: Chaperone]]
-[[Category: Group ii chaperonin]]
-[[Category: Methanococcus maripaludi]]
-[[Category: Mm-cpn]]
-[[Category: Nucleotide-binding]]
-[[Category: Protein folding]]
-[[Category: Single particle reconstruction]]