3a1y: Difference between revisions

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 <StructureSection load='3a1y' size='340' side='right'caption='[[3a1y]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3a1y]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A1Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3a1y]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A1Y FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH1998 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii']), PH1999 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</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]] 2.13&#8491;</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=3a1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a1y OCA], [https://pdbe.org/3a1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a1y RCSB], [https://www.ebi.ac.uk/pdbsum/3a1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a1y ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RL12_PYRHO RL12_PYRHO]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. The stalk complex of P.horikoshii binds to E.coli large subunits and confers on them the ability to interact with eukaryotic elongation factors. Each succesive L12 dimer bound along the P0 spine increases the GTPase activity of elongation factors and increases translation by reconsituted ribosomes.<ref>PMID:17804412</ref>  [[https://www.uniprot.org/uniprot/RL10_PYRHO RL10_PYRHO]] Forms the large subunit's ribosomal stalk, playing a central role in the interaction of the ribosome with elongation factors; the stalk complex of P.horikoshii binds to E.coli large subunits and confers on them the ability to interact with eukaryotic elongation factors. Each succesive L12 dimer bound along the P0 spine increases the GTPase activity of elongation factors and increases translation by reconsituted ribosomes, although the first site is the most stimulatory.<ref>PMID:17804412</ref>
+[https://www.uniprot.org/uniprot/RL12_PYRHO RL12_PYRHO] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. The stalk complex of P.horikoshii binds to E.coli large subunits and confers on them the ability to interact with eukaryotic elongation factors. Each succesive L12 dimer bound along the P0 spine increases the GTPase activity of elongation factors and increases translation by reconsituted ribosomes.<ref>PMID:17804412</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=3a1y ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The archaeal ribosomal stalk complex has been shown to have an apparently conserved functional structure with eukaryotic pentameric stalk complex; it provides access to eukaryotic elongation factors at levels comparable to that of the eukaryotic stalk. The crystal structure of the archaeal heptameric (P0(P1)(2)(P1)(2)(P1)(2)) stalk complex shows that the rRNA anchor protein P0 consists of an N-terminal rRNA-anchoring domain followed by three separated spine helices on which three P1 dimers bind. Based on the structure, we have generated P0 mutants depleted of any binding site(s) for P1 dimer(s). Factor-dependent GTPase assay of such mutants suggested that the first P1 dimer has higher activity than the others. Furthermore, we constructed a model of the archaeal 50 S with stalk complex by superposing the rRNA-anchoring domain of P0 on the archaeal 50 S. This model indicates that the C termini of P1 dimers where translation factors bind are all localized to the region between the stalk base of the 50 S and P0 spine helices. Together with the mutational experiments we infer that the functional significance of multiple copies of P1 is in creating a factor pool within a limited space near the stalk base of the ribosome.
-Structural basis for translation factor recruitment to the eukaryotic/archaeal ribosomes.,Naganuma T, Nomura N, Yao M, Mochizuki M, Uchiumi T, Tanaka I J Biol Chem. 2010 Feb 12;285(7):4747-56. Epub 2009 Dec 10. PMID:20007716<ref>PMID:20007716</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3a1y" style="background-color:#fffaf0;"></div>
 ==See Also==
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 __TOC__
 </StructureSection>
-[[Category: Pyrococcus shinkaii]]
 [[Category: Large Structures]]
-[[Category: Naganuma, T]]
+[[Category: Pyrococcus horikoshii]]
-[[Category: Nomura, N]]
+[[Category: Naganuma T]]
-[[Category: Tanaka, I]]
+[[Category: Nomura N]]
-[[Category: Uchiumi, T]]
+[[Category: Tanaka I]]
-[[Category: Yao, M]]
+[[Category: Uchiumi T]]
-[[Category: Yu, J]]
+[[Category: Yao M]]
-[[Category: Helix spin]]
+[[Category: Yu J]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Stalk]]