1mi6: Difference between revisions

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[[Image:1mi6.gif|left|200px]]


{{Structure
==Docking of the modified RF2 X-ray structure into the Low Resolution Cryo-EM map of RF2 E.coli 70S Ribosome==
|PDB= 1mi6 |SIZE=350|CAPTION= <scene name='initialview01'>1mi6</scene>
<SX load='1mi6' size='340' side='right' viewer='molstar' caption='[[1mi6]], [[Resolution|resolution]] 10.90&Aring;' scene=''>
|SITE=
== Structural highlights ==
|LIGAND=
<table><tr><td colspan='2'>[[1mi6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MI6 FirstGlance]. <br>
|ACTIVITY=
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 10.9&#8491;</td></tr>
|GENE=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mi6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mi6 OCA], [https://pdbe.org/1mi6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mi6 RCSB], [https://www.ebi.ac.uk/pdbsum/1mi6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mi6 ProSAT]</span></td></tr>
}}
</table>
 
== Function ==
'''Docking of the modified RF2 X-ray structure into the Low Resolution Cryo-EM map of RF2 E.coli 70S Ribosome'''
[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]]
==Overview==
Check<jmol>
Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mi/1mi6_consurf.spt"</scriptWhenChecked>
==About this Structure==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
1MI6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MI6 OCA].  
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==Reference==
</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=1mi6 ConSurf].
A cryo-electron microscopic study of ribosome-bound termination factor RF2., Rawat UB, Zavialov AV, Sengupta J, Valle M, Grassucci RA, Linde J, Vestergaard B, Ehrenberg M, Frank J, Nature. 2003 Jan 2;421(6918):87-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12511960 12511960]
<div style="clear:both"></div>
[[Category: Escherichia coli]]
__TOC__
[[Category: Single protein]]
</SX>
[[Category: Ehrenberg, M]]
[[Category: Escherichia coli K-12]]
[[Category: Frank, J.]]
[[Category: Large Structures]]
[[Category: Grassucci, R A.]]
[[Category: Ehrenberg M]]
[[Category: Linde, J.]]
[[Category: Frank J]]
[[Category: Rawat, U B.S.]]
[[Category: Grassucci RA]]
[[Category: Sengupta, J.]]
[[Category: Linde J]]
[[Category: Valle, M.]]
[[Category: Rawat UBS]]
[[Category: Vestergaard, B.]]
[[Category: Sengupta J]]
[[Category: Zavialov, A V.]]
[[Category: Valle M]]
[[Category: conformational change]]
[[Category: Vestergaard B]]
[[Category: release complex]]
[[Category: Zavialov AV]]
[[Category: rf2]]
 
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Retrieved from "https://proteopedia.org/1mi6"