1m90: Difference between revisions

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-[[Image:1m90.png|left|200px]]
-<!--
+==Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit==
-The line below this paragraph, containing "STRUCTURE_1m90", creates the "Structure Box" on the page.
+<StructureSection load='1m90' size='340' side='right'caption='[[1m90]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1m90]] 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=1M90 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M90 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <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>, <scene name='pdbligand=PHA:PHENYLALANINAL'>PHA</scene>, <scene name='pdbligand=SPS:SPARSOMYCIN'>SPS</scene></td></tr>
-{{STRUCTURE_1m90|  PDB=1m90  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m90 OCA], [https://pdbe.org/1m90 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m90 RCSB], [https://www.ebi.ac.uk/pdbsum/1m90 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m90 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/m9/1m90_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=1m90 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.
-===Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit===
+Structural insights into peptide bond formation.,Hansen JL, Schmeing TM, Moore PB, Steitz TA Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11670-5. Epub 2002 Aug 16. PMID:12185246<ref>PMID:12185246</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12185246}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1m90" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12185246 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_12185246}}
-==About this Structure==
-[[1m90]] is a 31 chain structure of [[Ribosomal protein L10]], [[Ribosomal protein L2]], [[Ribosomal protein L3]], [[Ribosomal protein L4]], [[Ribosomal protein L5]], [[Ribosomal protein L6]] and [[Ribosomal protein L7]] with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M90 OCA].
 ==See Also==
-*[[Ribosomal protein L10]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein L2]]
+== References ==
-*[[Ribosomal protein L3]]
+<references/>
-*[[Ribosomal protein L4]]
+__TOC__
-*[[Ribosomal protein L5]]
+</StructureSection>
-*[[Ribosomal protein L6]]
-*[[Ribosomal protein L7]]
-==Reference==
-<ref group="xtra">PMID:12185246</ref><references group="xtra"/>
 [[Category: Haloarcula marismortui]]
-[[Category: Hansen, J L.]]
+[[Category: Large Structures]]
-[[Category: Moore, P B.]]
+[[Category: Hansen JL]]
-[[Category: Schmeing, T M.]]
+[[Category: Moore PB]]
-[[Category: Steitz, T A.]]
+[[Category: Schmeing TM]]
-[[Category: P-site]]
+[[Category: Steitz TA]]
-[[Category: Ribosome]]
-[[Category: Sparsomycin]]