1q7y: Difference between revisions

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-[[Image:1q7y.png|left|200px]]
-{{STRUCTURE_1q7y|  PDB=1q7y  |  SCENE=  }}
+==Crystal Structure of CCdAP-Puromycin bound at the Peptidyl transferase center of the 50S ribosomal subunit==
+<StructureSection load='1q7y' size='340' side='right'caption='[[1q7y]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1q7y]] 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=1Q7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q7Y 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]] 3.2&#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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PUY:PUROMYCIN'>PUY</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=1q7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q7y OCA], [https://pdbe.org/1q7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q7y RCSB], [https://www.ebi.ac.uk/pdbsum/1q7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q7y ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448]
+== 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/q7/1q7y_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=1q7y 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.
-===Crystal Structure of CCdAP-Puromycin bound at the Peptidyl transferase center of 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>
-{{ABSTRACT_PUBMED_12185246}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1q7y" style="background-color:#fffaf0;"></div>
-[[1q7y]] is a 31 chain structure 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=1Q7Y OCA].
 ==See Also==
-*[[Ribosomal protein L10|Ribosomal protein L10]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein L13|Ribosomal protein L13]]
+== References ==
-*[[Ribosomal protein L14|Ribosomal protein L14]]
+<references/>
-*[[Ribosomal protein L15|Ribosomal protein L15]]
+__TOC__
-*[[Ribosomal protein L19|Ribosomal protein L19]]
+</StructureSection>
-*[[Ribosomal protein L2|Ribosomal protein L2]]
-*[[Ribosomal protein L21|Ribosomal protein L21]]
-*[[Ribosomal protein L3|Ribosomal protein L3]]
-*[[Ribosomal protein L34|Ribosomal protein L34]]
-*[[Ribosomal protein L5|Ribosomal protein L5]]
-*[[Ribosomal protein L6|Ribosomal protein L6]]
-*[[Ribosomal protein L7|Ribosomal protein L7]]
-==Reference==
-<ref group="xtra">PMID:012185246</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: Peptidyl transferase reaction]]
+[[Category: Steitz TA]]
-[[Category: Protein-protein complex]]
-[[Category: Protein-rna complex]]
-[[Category: Puromycin]]
-[[Category: Ribosome]]
-[[Category: Ribosome 50]]
-[[Category: Rna-rna complex]]