1njm: Difference between revisions

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OCA

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 ==The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin==
-<StructureSection load='1njm' size='340' side='right' caption='[[1njm]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
+<StructureSection load='1njm' size='340' side='right'caption='[[1njm]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1njm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1njm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] 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=1NJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPS:SPARSOMYCIN'>SPS</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.6&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPU:PUROMYCIN-5-MONOPHOSPHATE'>PPU</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PPU:PUROMYCIN-5-MONOPHOSPHATE'>PPU</scene>, <scene name='pdbligand=SPS:SPARSOMYCIN'>SPS</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1njn|1njn]], [[1njo|1njo]], [[1njp|1njp]], [[1k01|1k01]], [[1jzx|1jzx]], [[1jzy|1jzy]], [[1jzz|1jzz]], [[1k00|1k00]], [[1nkw|1nkw]]</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=1njm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njm OCA], [https://pdbe.org/1njm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njm RCSB], [https://www.ebi.ac.uk/pdbsum/1njm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njm ProSAT]</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=1njm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njm RCSB], [http://www.ebi.ac.uk/pdbsum/1njm PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RL25_DEIRA RL25_DEIRA]] This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit. This protein has three domains. The N-terminal one is bound on the solvent face, the middle domain fills the space between the 5S rRNA and the L11 arm contacting the 23S rRNA while the C-terminal domain is on the edge of the intersubunit interface and contacts the A site. The protein conformation changes upon binding of a tRNA mimic to the A site, although the mimic does not interact directly with CTC itself, consistent with CTCs presumed role in moderating A site binding.[HAMAP-Rule:MF_01334] [[http://www.uniprot.org/uniprot/RL16_DEIRA RL16_DEIRA]] Binds the 5S and 23S rRNAs and is also seen to make contacts with the A and P site tRNAs. Interacts with A site tRNA mimics, and is probably one of the key factors, along with a helix of the 23S rRNA, in positioning tRNA stems in the peptidyl-transferase center.[HAMAP-Rule:MF_01342]
+[https://www.uniprot.org/uniprot/RL16_DEIRA RL16_DEIRA] Binds the 5S and 23S rRNAs and is also seen to make contacts with the A and P site tRNAs. Interacts with A site tRNA mimics, and is probably one of the key factors, along with a helix of the 23S rRNA, in positioning tRNA stems in the peptidyl-transferase center.[HAMAP-Rule:MF_01342]
 == 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/nj/1njm_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/1njm_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=1njm ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1njm" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Ribosomal protein L16|Ribosomal protein L16]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==
 <references/>
@@ Line 36: / Line 38: @@
 </StructureSection>
 [[Category: Deinococcus radiodurans]]
-[[Category: Agmon, I]]
+[[Category: Large Structures]]
-[[Category: Bartels, H]]
+[[Category: Synthetic construct]]
-[[Category: Bashan, A]]
+[[Category: Agmon I]]
-[[Category: Berisio, R]]
+[[Category: Bartels H]]
-[[Category: Hansen, H A]]
+[[Category: Bashan A]]
-[[Category: Harms, J M]]
+[[Category: Berisio R]]
-[[Category: Schluenzen, F]]
+[[Category: Hansen HA]]
-[[Category: Yonath, A]]
+[[Category: Harms JM]]
-[[Category: Zarivatch, R]]
+[[Category: Schluenzen F]]
-[[Category: Peptide bond formation]]
+[[Category: Yonath A]]
-[[Category: Peptidyl-transferase]]
+[[Category: Zarivatch R]]
-[[Category: Puromycin]]
-[[Category: Ribosome]]
-[[Category: Sparsomycin]]
-[[Category: Trna]]