1q3r: Difference between revisions

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-[[Image:1q3r.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1q3r", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1q3r|  PDB=1q3r  |  SCENE=  }}
-'''Crystal structure of the chaperonin from Thermococcus strain KS-1 (nucleotide-free form of single mutant)'''
+==Crystal structure of the chaperonin from Thermococcus strain KS-1 (nucleotide-free form of single mutant)==
+<StructureSection load='1q3r' size='340' side='right'caption='[[1q3r]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1q3r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_sp._JCM_11816 Thermococcus sp. JCM 11816]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q3R FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1q3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3r OCA], [https://pdbe.org/1q3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q3r RCSB], [https://www.ebi.ac.uk/pdbsum/1q3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3r ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/THSA_THEK1 THSA_THEK1] Molecular chaperone; binds unfolded polypeptides in vitro, and has a weak ATPase activity.
+== 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/q3/1q3r_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/main_output.php?pdb_ID=1q3r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of the group II chaperonins consisting of the alpha subunit with amino acid substitutions of G65C and/or I125T from the hyperthermophilic archaeum Thermococcus strain KS-1 were determined. These mutants have been shown to be active in ATP hydrolysis but inactive in protein folding. The structures were shown to be double-ring hexadecamers in an extremely closed form, which was consistent with the crystal structure of native alpha8beta8-chaperonin from Thermoplasma acidophilum. Comparisons of the present structures with the atomic structures of the GroEL14-GroES7-(ADP)7 complex revealed that the deficiency in protein-folding activity with the G65C amino acid substitution is caused by the steric hindrance of the local conformational change in an equatorial domain. We concluded that this mutant chaperonin with G65C substitution is deprived of the smooth conformational change in the refolding-reaction cycle. We obtained a new form of crystal with a distinct space group at a lower concentration of sulfate ion in the presence of nucleotide. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion. Such subunit rotation has never been characterized in group II chaperonins. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion.
-==Overview==
+Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms.,Shomura Y, Yoshida T, Iizuka R, Maruyama T, Yohda M, Miki K J Mol Biol. 2004 Jan 30;335(5):1265-78. PMID:14729342<ref>PMID:14729342</ref>
-The crystal structures of the group II chaperonins consisting of the alpha subunit with amino acid substitutions of G65C and/or I125T from the hyperthermophilic archaeum Thermococcus strain KS-1 were determined. These mutants have been shown to be active in ATP hydrolysis but inactive in protein folding. The structures were shown to be double-ring hexadecamers in an extremely closed form, which was consistent with the crystal structure of native alpha8beta8-chaperonin from Thermoplasma acidophilum. Comparisons of the present structures with the atomic structures of the GroEL14-GroES7-(ADP)7 complex revealed that the deficiency in protein-folding activity with the G65C amino acid substitution is caused by the steric hindrance of the local conformational change in an equatorial domain. We concluded that this mutant chaperonin with G65C substitution is deprived of the smooth conformational change in the refolding-reaction cycle. We obtained a new form of crystal with a distinct space group at a lower concentration of sulfate ion in the presence of nucleotide. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion. Such subunit rotation has never been characterized in group II chaperonins. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Q3R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_sp. Thermococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3R OCA].
+</div>
+<div class="pdbe-citations 1q3r" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms., Shomura Y, Yoshida T, Iizuka R, Maruyama T, Yohda M, Miki K, J Mol Biol. 2004 Jan 30;335(5):1265-78. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14729342 14729342]
+*[[Chaperonin 3D structures|Chaperonin 3D structures]]
-[[Category: Chaperonin ATPase]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Thermococcus sp.]]
+__TOC__
-[[Category: Iizuka, R.]]
+</StructureSection>
-[[Category: Maruyama, T.]]
+[[Category: Large Structures]]
-[[Category: Miki, K.]]
+[[Category: Thermococcus sp. JCM 11816]]
-[[Category: Shomura, Y.]]
+[[Category: Iizuka R]]
-[[Category: Yohda, M.]]
+[[Category: Maruyama T]]
-[[Category: Yoshida, T.]]
+[[Category: Miki K]]
-[[Category: Chaperone]]
+[[Category: Shomura Y]]
-[[Category: Chaperonin]]
+[[Category: Yohda M]]
-[[Category: Thermosome]]
+[[Category: Yoshida T]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 05:49:53 2008''