1jj2: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1jj2.jpg|left|200px]]<br /><applet load="1jj2" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1jj2, resolution 2.40&Aring;" />
-'''Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution'''<br />
-==Overview==
+==Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution==
-Analysis of the Haloarcula marismortui large ribosomal subunit has, revealed a common RNA structure that we call the kink-turn, or K-turn. The, six K-turns in H.marismortui 23S rRNA superimpose with an r.m.s.d. of 1.7, A. There are two K-turns in the structure of Thermus thermophilus 16S, rRNA, and the structures of U4 snRNA and L30e mRNA fragments form K-turns., The structure has a kink in the phosphodiester backbone that causes a, sharp turn in the RNA helix. Its asymmetric internal loop is flanked by, C-G base pairs on one side and sheared G-A base pairs on the other, with, an A-minor interaction between these two helical stems. A derived, consensus secondary structure for the K-turn includes 10 consensus, nucleotides out of 15, and predicts its presence in the 5'-UTR of L10, mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP. Five, K-turns in 23S rRNA interact with nine proteins. While the observed, K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way.
+<StructureSection load='1jj2' size='340' side='right'caption='[[1jj2]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1jj2]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JJ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JJ2 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]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1jj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jj2 OCA], [https://pdbe.org/1jj2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jj2 RCSB], [https://www.ebi.ac.uk/pdbsum/1jj2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jj2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]
+== 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/jj/1jj2_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=1jj2 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-JJ2 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] with MG, K, NA, CD and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JJ2 OCA].
+*[[Lac repressor|Lac repressor]]
+*[[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit of Haloarcula]]
-==Reference==
+*[[Ribosome|Ribosome]]
-The kink-turn: a new RNA secondary structure motif., Klein DJ, Schmeing TM, Moore PB, Steitz TA, EMBO J. 2001 Aug 1;20(15):4214-21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11483524 11483524]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+__TOC__
+</StructureSection>
 [[Category: Haloarcula marismortui]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Klein, D.J.]]
+[[Category: Klein DJ]]
-[[Category: Moore, P.B.]]
+[[Category: Moore PB]]
-[[Category: Schmeing, T.M.]]
+[[Category: Schmeing TM]]
-[[Category: Steitz, T.A.]]
+[[Category: Steitz TA]]
-[[Category: CD]]
-[[Category: CL]]
-[[Category: K]]
-[[Category: MG]]
-[[Category: NA]]
-[[Category: protein-protein]]
-[[Category: protein-rna]]
-[[Category: ribosome assembly]]
-[[Category: rna-rna]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:18:43 2007''