1p6v

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[[Image:1p6v.gif|left|200px]]
 
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{{Structure
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==Crystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB==
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|PDB= 1p6v |SIZE=350|CAPTION= <scene name='initialview01'>1p6v</scene>, resolution 3.20&Aring;
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<StructureSection load='1p6v' size='340' side='right'caption='[[1p6v]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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<table><tr><td colspan='2'>[[1p6v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P6V FirstGlance]. <br>
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|ACTIVITY=
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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]] 3.2&#8491;</td></tr>
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|GENE= SMPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p6v OCA], [https://pdbe.org/1p6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p6v RCSB], [https://www.ebi.ac.uk/pdbsum/1p6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p6v ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p6v OCA], [http://www.ebi.ac.uk/pdbsum/1p6v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1p6v RCSB]</span>
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[https://www.uniprot.org/uniprot/SSRP_AQUAE SSRP_AQUAE] Binds specifically to the SsrA RNA (tmRNA) and is required for stable association of SsrA with ribosomes.
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}}
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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'''Crystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB'''
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p6/1p6v_consurf.spt"</scriptWhenChecked>
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==Overview==
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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Accurate translation of genetic information into protein sequence depends on complete messenger RNA molecules. Truncated mRNAs cause synthesis of defective proteins, and arrest ribosomes at the end of their incomplete message. In bacteria, a hybrid RNA molecule that combines the functions of both transfer and messenger RNAs (called tmRNA) rescues stalled ribosomes, and targets aberrant, partially synthesized, proteins for proteolytic degradation. Here we report the 3.2-A-resolution structure of the tRNA-like domain of tmRNA (tmRNA(Delta)) in complex with small protein B (SmpB), a protein essential for biological functions of tmRNA. We find that the flexible RNA molecule adopts an open L-shaped conformation and SmpB binds to its elbow region, stabilizing the single-stranded D-loop in an extended conformation. The most striking feature of the structure of tmRNA(Delta) is a 90 degrees rotation of the TPsiC-arm around the helical axis. Owing to this unusual conformation, the SmpB-tmRNA(Delta) complex positioned into the A-site of the ribosome orients SmpB towards the small ribosomal subunit, and directs tmRNA towards the elongation-factor binding region of the ribosome. On the basis of this structure, we propose a model for the binding of tmRNA on the ribosome.
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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==About this Structure==
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</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=1p6v ConSurf].
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1P6V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P6V OCA].
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<div style="clear:both"></div>
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB., Gutmann S, Haebel PW, Metzinger L, Sutter M, Felden B, Ban N, Nature. 2003 Aug 7;424(6949):699-703. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12904796 12904796]
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[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Ban, N.]]
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[[Category: Ban N]]
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[[Category: Felden, B.]]
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[[Category: Felden B]]
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[[Category: Gutmann, S.]]
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[[Category: Gutmann S]]
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[[Category: Haebel, P W.]]
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[[Category: Haebel PW]]
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[[Category: Metzinger, L.]]
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[[Category: Metzinger L]]
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[[Category: Sutter, M.]]
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[[Category: Sutter M]]
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[[Category: protein-rna complex]]
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[[Category: smpb]]
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[[Category: tmrna]]
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[[Category: trans-translation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:55:42 2008''
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Current revision

Crystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB

PDB ID 1p6v

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