2fvo: Difference between revisions

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New page: left|200px<br /><applet load="2fvo" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fvo" /> '''Docking of the modified RF1 X-ray structure ...
 
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[[Image:2fvo.gif|left|200px]]<br /><applet load="2fvo" size="450" color="white" frame="true" align="right" spinBox="true"
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'''Docking of the modified RF1 X-ray structure into the Low Resolution Cryo-EM map of E.coli 70S Ribosome bound with RF1'''<br />


==Overview==
==Docking of the modified RF1 X-ray structure into the Low Resolution Cryo-EM map of E.coli 70S Ribosome bound with RF1==
In eubacteria, termination of translation is signaled by any one of the, stop codons UAA, UAG, and UGA moving into the ribosomal A site. Two, release factors, RF1 and RF2, recognize and bind to the stop codons with, different affinities and trigger the hydrolysis of the ester bond that, links the polypeptide with the P-site tRNA. Cryo-electron microscopy, (cryo-EM) results obtained in this study show that ribosome-bound RF1 is, in an open conformation, unlike the closed conformation observed in the, crystal structure of the free factor, allowing its simultaneous access to, both the decoding center and the peptidyl-transferase center. These, results are similar to those obtained for RF2, but there is an important, difference in how the factors bind to protein L11, which forms part of the, GTPase-associated center of the large ribosomal subunit. The difference in, the binding position, C-terminal domain for RF2 versus N-terminal domain, for RF1, explains a body of L11 mutation studies that revealed, differential effects on the activity of the two factors. Very recent data, obtained with small-angle X-ray scattering now reveal that the solution, structure of RF1 is open, as here seen on the ribosome by cryo-EM, and not, closed, as seen in the crystal.
<SX load='2fvo' size='340' side='right' viewer='molstar' caption='[[2fvo]], [[Resolution|resolution]] 12.80&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2fvo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FVO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FVO FirstGlance]. <br>
2FVO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FVO OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 12.8&#8491;</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=2fvo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fvo OCA], [https://pdbe.org/2fvo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fvo RCSB], [https://www.ebi.ac.uk/pdbsum/2fvo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fvo ProSAT]</span></td></tr>
==Reference==
</table>
Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM., Rawat U, Gao H, Zavialov A, Gursky R, Ehrenberg M, Frank J, J Mol Biol. 2006 Apr 7;357(4):1144-53. Epub 2006 Jan 30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16476444 16476444]
== Function ==
[[Category: Single protein]]
[https://www.uniprot.org/uniprot/RF1_THEMA RF1_THEMA] Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA (By similarity).
== 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/fv/2fvo_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=2fvo ConSurf].
<div style="clear:both"></div>
__TOC__
</SX>
[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
[[Category: Ehrenberg, M.]]
[[Category: Ehrenberg M]]
[[Category: Frank, J.]]
[[Category: Frank J]]
[[Category: Gao, H.]]
[[Category: Gao H]]
[[Category: Gursky, R.]]
[[Category: Gursky R]]
[[Category: Rawat, U.]]
[[Category: Rawat U]]
[[Category: Zavialov, A.]]
[[Category: Zavialov A]]
[[Category: rf1 ribosome cryo-em]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:47:45 2007''

Latest revision as of 12:25, 14 February 2024

Docking of the modified RF1 X-ray structure into the Low Resolution Cryo-EM map of E.coli 70S Ribosome bound with RF1Docking of the modified RF1 X-ray structure into the Low Resolution Cryo-EM map of E.coli 70S Ribosome bound with RF1

2fvo, resolution 12.80Å

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