2p8y: Difference between revisions
From Proteopedia
Jump to navigationJump to search
New page: left|200px<br /><applet load="2p8y" size="450" color="white" frame="true" align="right" spinBox="true" caption="2p8y" /> '''Fitted structure of ADPR-eEF2 in the 80S:ADP... |
No edit summary |
||
| (19 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
== | ==Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDP:sordarin cryo-EM reconstruction== | ||
On the basis of kinetic data on ribosome protein synthesis, the mechanical | <SX load='2p8y' size='340' side='right' viewer='molstar' caption='[[2p8y]], [[Resolution|resolution]] 11.70Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2p8y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P8Y 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]] 11.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=DDE:{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM'>DDE</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=SO1:(1S,3R,3aR,4S,4aR,7R,7aR,8aS)-8a-{[(6-deoxy-4-O-methyl-beta-D-altropyranosyl)oxy]methyl}-4-formyl-7-methyl-3-(1-methylethyl)decahydro-1,4-methano-s-indacene-3a(1H)-carboxylic+acid'>SO1</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=2p8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8y OCA], [https://pdbe.org/2p8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p8y RCSB], [https://www.ebi.ac.uk/pdbsum/2p8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8y ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/EF2_YEAST EF2_YEAST] | |||
== 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/p8/2p8y_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2p8y ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
On the basis of kinetic data on ribosome protein synthesis, the mechanical energy for translocation of the mRNA-tRNA complex is thought to be provided by GTP hydrolysis of an elongation factor (eEF2 in eukaryotes, EF-G in bacteria). We have obtained cryo-EM reconstructions of eukaryotic ribosomes complexed with ADP-ribosylated eEF2 (ADPR-eEF2), before and after GTP hydrolysis, providing a structural basis for analyzing the GTPase-coupled mechanism of translocation. Using the ADP-ribosyl group as a distinct marker, we observe conformational changes of ADPR-eEF2 that are due strictly to GTP hydrolysis. These movements are likely representative of native eEF2 motions in a physiological context and are sufficient to uncouple the mRNA-tRNA complex from two universally conserved bases in the ribosomal decoding center (A1492 and A1493 in Escherichia coli) during translocation. Interpretation of these data provides a detailed two-step model of translocation that begins with the eEF2/EF-G binding-induced ratcheting motion of the small ribosomal subunit. GTP hydrolysis then uncouples the mRNA-tRNA complex from the decoding center so translocation of the mRNA-tRNA moiety may be completed by a head rotation of the small subunit. | |||
Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation.,Taylor DJ, Nilsson J, Merrill AR, Andersen GR, Nissen P, Frank J EMBO J. 2007 May 2;26(9):2421-31. Epub 2007 Apr 19. PMID:17446867<ref>PMID:17446867</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2p8y" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Elongation factor 3D structures|Elongation factor 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</SX> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Andersen GR]] | |||
[[Category: Andersen | [[Category: Frank J]] | ||
[[Category: Frank | [[Category: Merrill AR]] | ||
[[Category: Merrill | [[Category: Nilsson J]] | ||
[[Category: Nilsson | [[Category: Nissen P]] | ||
[[Category: Nissen | [[Category: Taylor DJ]] | ||
[[Category: Taylor | |||
