3tg8: Difference between revisions

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 <StructureSection load='3tg8' size='340' side='right'caption='[[3tg8]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3tg8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TG8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3tg8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TG8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ad2|1ad2]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rplA, rpl1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=3tg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tg8 OCA], [https://pdbe.org/3tg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tg8 RCSB], [https://www.ebi.ac.uk/pdbsum/3tg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tg8 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RL1_THETH RL1_THETH]] The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release (By similarity). Binds directly to 23S rRNA.[HAMAP-Rule:MF_01318]  Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318]
+[https://www.uniprot.org/uniprot/RL1_THET8 RL1_THET8] Directly binds to 23S rRNA. Forms what is known as the L1 stalk, which protrudes beyond the 70S ribosome surface. The stalk is preferentially stabilized in 70S versus 50S crystals. Interacts with the E site tRNA, blocking the exit path. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_01318_B]  Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318_B]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Ribosomal protein L1 consists of two domains connected by two oppositely directed fragments of the polypeptide chain in a hinge-resembling fashion. The domain arrangement determines the overall shape of the protein, corresponding to an open or a closed conformation. Ribosomal L1 proteins from archaea demonstrate the open conformation in both isolated and RNA-bound forms. RNA-free ribosomal L1 proteins from bacteria display the closed conformation, whereas in complex with RNA these proteins exist in an open conformation similar to their archaeal counterparts. Analysis of all available L1 amino-acid sequences shows that in comparison to the archaeal proteins, the bacterial proteins possess an extra residue in one of the two interdomain fragments which could be responsible for their closed conformation. To verify this suggestion, a Thermus thermophilus L1 mutant lacking one residue in the fragment corresponding to the hinge was obtained and its crystal structure was solved. It was found that this mutation transformed the closed conformation of the bacterial L1 protein into an open conformation similar to that of the archaeal L1 proteins.
-Structural analysis of interdomain mobility in ribosomal L1 proteins.,Tishchenko S, Nikonova E, Kostareva O, Gabdulkhakov A, Piendl W, Nevskaya N, Garber M, Nikonov S Acta Crystallogr D Biol Crystallogr. 2011 Dec;67(Pt 12):1023-7. Epub 2011 Nov 5. PMID:22120739<ref>PMID:22120739</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3tg8" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Ribosomal protein L1|Ribosomal protein L1]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
 [[Category: Large Structures]]
-[[Category: Gabdulkhakov, A G]]
+[[Category: Thermus thermophilus]]
-[[Category: Nevskaya, N A]]
+[[Category: Gabdulkhakov AG]]
-[[Category: Nikonov, S V]]
+[[Category: Nevskaya NA]]
-[[Category: Mutant]]
+[[Category: Nikonov SV]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome]]
-[[Category: Rna binding]]