2r1c: Difference between revisions

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 ==Coordinates of the thermus thermophilus ribosome binding factor A (RbfA) homology model as fitted into the CRYO-EM map of a 30S-RBFA complex==
-<StructureSection load='2r1c' size='340' side='right' caption='[[2r1c]], [[Resolution|resolution]] 12.50&Aring;' scene=''>
+<SX load='2r1c' size='340' side='right' viewer='molstar' caption='[[2r1c]], [[Resolution|resolution]] 12.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2r1c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2r1c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1C FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jos|1jos]], [[2dyj|2dyj]], [[2r1g|2r1g]]</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]] 12.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA0907 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=2r1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1c OCA], [https://pdbe.org/2r1c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1c RCSB], [https://www.ebi.ac.uk/pdbsum/2r1c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1c ProSAT], [https://www.topsan.org/Proteins/RSGI/2r1c TOPSAN]</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=2r1c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r1c RCSB], [http://www.ebi.ac.uk/pdbsum/2r1c PDBsum], [http://www.topsan.org/Proteins/RSGI/2r1c TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RBFA_THET8 RBFA_THET8] One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes) (PubMed:17996707). Required for efficient processing of 16S rRNA. Probably interacts with the 5'-terminal helix region of 16S rRNA, bringing together different domains of the 30S ribosomal subunit which aids assembly (PubMed:17996707).<ref>PMID:17996707</ref>
 == 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/r1/2r1c_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/2r1c_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=2r1c ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock.
-Structural aspects of RbfA action during small ribosomal subunit assembly.,Datta PP, Wilson DN, Kawazoe M, Swami NK, Kaminishi T, Sharma MR, Booth TM, Takemoto C, Fucini P, Yokoyama S, Agrawal RK Mol Cell. 2007 Nov 9;28(3):434-45. PMID:17996707<ref>PMID:17996707</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Thermus thermophilus]]
+[[Category: Large Structures]]
-[[Category: Agrawal, R K]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Booth, T M]]
+[[Category: Agrawal RK]]
-[[Category: Datta, P P]]
+[[Category: Booth TM]]
-[[Category: Fucini, P]]
+[[Category: Datta PP]]
-[[Category: Kaminishi, T]]
+[[Category: Fucini P]]
-[[Category: Kawazoe, M]]
+[[Category: Kaminishi T]]
-[[Category: Sharma, M R]]
+[[Category: Kawazoe M]]
-[[Category: Swami, N K]]
+[[Category: Sharma MR]]
-[[Category: Takemoto, C]]
+[[Category: Swami NK]]
-[[Category: Wilson, D N]]
+[[Category: Takemoto C]]
-[[Category: Yokoyama, S]]
+[[Category: Wilson DN]]
-[[Category: Helix-kink-helix]]
+[[Category: Yokoyama S]]
-[[Category: Kh domain]]
-[[Category: Rna binding protein]]
-[[Category: Rrna processing]]