2r1g: Difference between revisions

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OCA

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 ==Coordinates of the thermus thermophilus 30S components neighboring RbfA as obtained by fitting into the CRYO-EM map of A 30S-RBFA complex==
-<StructureSection load='2r1g' size='340' side='right' caption='[[2r1g]], [[Resolution|resolution]] 12.50&Aring;' scene=''>
+<SX load='2r1g' size='340' side='right' viewer='molstar' caption='[[2r1g]], [[Resolution|resolution]] 12.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2r1g]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2r1g]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1G FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1j5e|1j5e]], [[2r1c|2r1c]], [[2dyj|2dyj]]</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><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpsM, rps13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 Thermus thermophilus HB27]), rpsI, rps9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 Thermus thermophilus HB27]), rpsL, rps12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 Thermus thermophilus HB27])</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=2r1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1g OCA], [https://pdbe.org/2r1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1g RCSB], [https://www.ebi.ac.uk/pdbsum/2r1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1g ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r1g RCSB], [http://www.ebi.ac.uk/pdbsum/2r1g PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity).
 == 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/r1/2r1g_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/2r1g_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=2r1g 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>
 ==See Also==
@@ Line 30: / Line 24: @@
 *[[Ribosomal protein S13|Ribosomal protein S13]]
 *[[Ribosomal protein S9|Ribosomal protein S9]]
-== References ==
-<references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Thermus thermophilus hb27]]
+[[Category: Large Structures]]
-[[Category: Agrawal, R K.]]
+[[Category: Synthetic construct]]
-[[Category: Booth, T M.]]
+[[Category: Thermus thermophilus HB27]]
-[[Category: Datta, P P.]]
+[[Category: Agrawal RK]]
-[[Category: Fucini, P.]]
+[[Category: Booth TM]]
-[[Category: Kaminishi, T.]]
+[[Category: Datta PP]]
-[[Category: Kawazoe, M.]]
+[[Category: Fucini P]]
-[[Category: Sharma, M R.]]
+[[Category: Kaminishi T]]
-[[Category: Swami, N K.]]
+[[Category: Kawazoe M]]
-[[Category: Takemoto, C.]]
+[[Category: Sharma MR]]
-[[Category: Wilson, D N.]]
+[[Category: Swami NK]]
-[[Category: Yokoyama, S.]]
+[[Category: Takemoto C]]
-[[Category: 30s ribosome maturation protein rbfa]]
+[[Category: Wilson DN]]
-[[Category: 30s-rbfa complex]]
+[[Category: Yokoyama S]]
-[[Category: Antibiotic resistance]]
-[[Category: Cold shock response protein rbfa]]
-[[Category: Rbfa binding site on the 30]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosomal protein-rna complex]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Trna-binding]]