1ml5: Difference between revisions

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New page: left|200px<br /><applet load="1ml5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ml5" /> '''Structure of the E. coli ribosomal terminati...
 
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[[Image:1ml5.gif|left|200px]]<br /><applet load="1ml5" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ml5" />
'''Structure of the E. coli ribosomal termination complex with release factor 2'''<br />


==Overview==
==Structure of the E. coli ribosomal termination complex with release factor 2==
Termination of protein synthesis occurs when the messenger RNA presents a, stop codon in the ribosomal aminoacyl (A) site. Class I release factor, proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide, motifs, leading to release of the completed polypeptide chain from its, covalent attachment to transfer RNA in the ribosomal peptidyl (P) site., Class I RFs possess a conserved GGQ amino-acid motif that is thought to be, involved directly in protein-transfer-RNA bond hydrolysis. Crystal, structures of bacterial and eukaryotic class I RFs have been determined, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis, remains unclear. Here we present the structure of the Escherichia coli, ribosome in a post-termination complex with RF2, obtained by, single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S, and RF2 structures into the electron density map reveals that RF2 adopts a, different conformation on the ribosome when compared with the crystal, structure of the isolated protein. The amino-terminal helical domain of, RF2 contacts the factor-binding site of the ribosome, the 'SPF' loop of, the protein is situated close to the mRNA, and the GGQ-containing domain, of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting, the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA, molecule in the A site. Translational termination in eukaryotes is likely, to be based on a similar mechanism.
<SX load='1ml5' size='340' side='right' viewer='molstar' caption='[[1ml5]], [[Resolution|resolution]] 14.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ml5]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ML5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ML5 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 14&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=1ml5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ml5 OCA], [https://pdbe.org/1ml5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ml5 RCSB], [https://www.ebi.ac.uk/pdbsum/1ml5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ml5 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RF2_ECOLI RF2_ECOLI] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.[HAMAP-Rule:MF_00094]
== 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/ml/1ml5_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=1ml5 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1ML5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ML5 OCA].
*[[MHC 3D structures|MHC 3D structures]]
 
*[[MHC I 3D structures|MHC I 3D structures]]
==Reference==
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
Structure of the Escherichia coli ribosomal termination complex with release factor 2., Klaholz BP, Pape T, Zavialov AV, Myasnikov AG, Orlova EV, Vestergaard B, Ehrenberg M, van Heel M, Nature. 2003 Jan 2;421(6918):90-4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12511961 12511961]
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
__TOC__
</SX>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Ehrenberg, M.]]
[[Category: Ehrenberg M]]
[[Category: Heel, M.van.]]
[[Category: Klaholz BP]]
[[Category: Klaholz, B.P.]]
[[Category: Myasnikov AG]]
[[Category: Myasnikov, A.G.]]
[[Category: Orlova EV]]
[[Category: Orlova, E.V.]]
[[Category: Pape T]]
[[Category: Pape, T.]]
[[Category: Vestergaard B]]
[[Category: Vestergaard, B.]]
[[Category: Zavialov AV]]
[[Category: Zavialov, A.V.]]
[[Category: Van Heel M]]
[[Category: angular reconstitution]]
[[Category: cryo-eletron microscopy]]
[[Category: e. coli]]
[[Category: release factor]]
[[Category: ribosome]]
[[Category: termination of protein synthesis]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:29:43 2007''

Latest revision as of 10:45, 14 February 2024

Structure of the E. coli ribosomal termination complex with release factor 2Structure of the E. coli ribosomal termination complex with release factor 2

1ml5, resolution 14.00Å

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