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1njp

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Current revision (09:20, 16 August 2023) (edit) (undo)
 
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<StructureSection load='1njp' size='340' side='right'caption='[[1njp]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
<StructureSection load='1njp' size='340' side='right'caption='[[1njp]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1njp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJP FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1njp]] 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=1NJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJP FirstGlance]. <br>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1njm|1njm]], [[1njn|1njn]], [[1njo|1njo]], [[1k01|1k01]], [[1jzx|1jzx]], [[1jzy|1jzy]], [[1jzz|1jzz]], [[1k00|1k00]], [[1nkw|1nkw]]</div></td></tr>
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<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></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=1njp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njp OCA], [https://pdbe.org/1njp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njp RCSB], [https://www.ebi.ac.uk/pdbsum/1njp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njp ProSAT]</span></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=1njp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njp OCA], [https://pdbe.org/1njp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njp RCSB], [https://www.ebi.ac.uk/pdbsum/1njp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njp ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://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] [[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]
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[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Agmon, I]]
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[[Category: Synthetic construct]]
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[[Category: Bartels, H]]
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[[Category: Agmon I]]
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[[Category: Bashan, A]]
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[[Category: Bartels H]]
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[[Category: Berisio, R]]
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[[Category: Bashan A]]
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[[Category: Hansen, H A]]
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[[Category: Berisio R]]
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[[Category: Harms, J M]]
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[[Category: Hansen HA]]
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[[Category: Schluenzen, F]]
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[[Category: Harms JM]]
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[[Category: Yonath, A]]
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[[Category: Schluenzen F]]
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[[Category: Zarivatch, R]]
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[[Category: Yonath A]]
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[[Category: Peptide bond formation]]
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[[Category: Zarivatch R]]
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[[Category: Peptidyl-transferase]]
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[[Category: Puromycin]]
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[[Category: Ribosome]]
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[[Category: Sparsomycin]]
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[[Category: Trna]]
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Current revision

The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM)

PDB ID 1njp

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OCA

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