3ep2: Difference between revisions

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[[Image:3ep2.png|left|200px]]
==Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM==
<StructureSection load='3ep2' size='340' side='right' caption='[[3ep2]], [[Resolution|resolution]] 9.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3ep2]] is a 9 chain structure with sequence from [http://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=3EP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EP2 FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2avy|2avy]], [[2aw4|2aw4]], [[1qza|1qza]], [[1ob2|1ob2]], [[3eq3|3eq3]], [[3eq4|3eq4]]</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ep2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ep2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ep2 RCSB], [http://www.ebi.ac.uk/pdbsum/3ep2 PDBsum]</span></td></tr>
<table>
== 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/ep/3ep2_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of the kirromycin-stalled ribosome bound with ternary complexes containing Phe-tRNA(Phe), Trp-tRNA(Trp), or Leu-tRNA(LeuI). The three maps suggest a common binding manner of cognate aa-tRNAs in their specific binding with both the ribosome and EF-Tu. All three aa-tRNAs have the same 'loaded spring' conformation with a kink and twist between the D-stem and anticodon stem. The three complexes are similarly integrated in an interaction network, extending from the anticodon loop through h44 and protein S12 to the EF-Tu-binding CCA end of aa-tRNA, proposed to signal cognate codon-anticodon interaction to the GTPase centre and tune the accuracy of aa-tRNA selection.


{{STRUCTURE_3ep2|  PDB=3ep2  |  SCENE=  }}
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.,Li W, Agirrezabala X, Lei J, Bouakaz L, Brunelle JL, Ortiz-Meoz RF, Green R, Sanyal S, Ehrenberg M, Frank J EMBO J. 2008 Dec 17;27(24):3322-31. Epub 2008 Nov 20. PMID:19020518<ref>PMID:19020518</ref>


===Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_19020518}}
 
==About this Structure==
[[3ep2]] is a 9 chain structure with sequence from [http://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=3EP2 OCA].


==See Also==
==See Also==
*[[Elongation factor|Elongation factor]]
*[[Ribosomal protein L11|Ribosomal protein L11]]
*[[Ribosomal protein L11|Ribosomal protein L11]]
*[[Ribosomal protein S12|Ribosomal protein S12]]
== References ==
 
<references/>
==Reference==
__TOC__
<ref group="xtra">PMID:019020518</ref><references group="xtra"/>
</StructureSection>
[[Category: Escherichia coli k-12]]
[[Category: Escherichia coli k-12]]
[[Category: Agirrezabala, X.]]
[[Category: Agirrezabala, X.]]

Revision as of 16:19, 29 September 2014

Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EMModel of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM

Structural highlights

3ep2 is a 9 chain structure with sequence from Escherichia coli k-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:2avy, 2aw4, 1qza, 1ob2, 3eq3, 3eq4
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of the kirromycin-stalled ribosome bound with ternary complexes containing Phe-tRNA(Phe), Trp-tRNA(Trp), or Leu-tRNA(LeuI). The three maps suggest a common binding manner of cognate aa-tRNAs in their specific binding with both the ribosome and EF-Tu. All three aa-tRNAs have the same 'loaded spring' conformation with a kink and twist between the D-stem and anticodon stem. The three complexes are similarly integrated in an interaction network, extending from the anticodon loop through h44 and protein S12 to the EF-Tu-binding CCA end of aa-tRNA, proposed to signal cognate codon-anticodon interaction to the GTPase centre and tune the accuracy of aa-tRNA selection.

Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.,Li W, Agirrezabala X, Lei J, Bouakaz L, Brunelle JL, Ortiz-Meoz RF, Green R, Sanyal S, Ehrenberg M, Frank J EMBO J. 2008 Dec 17;27(24):3322-31. Epub 2008 Nov 20. PMID:19020518[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Li W, Agirrezabala X, Lei J, Bouakaz L, Brunelle JL, Ortiz-Meoz RF, Green R, Sanyal S, Ehrenberg M, Frank J. Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM. EMBO J. 2008 Dec 17;27(24):3322-31. Epub 2008 Nov 20. PMID:19020518 doi:10.1038/emboj.2008.243

3ep2, resolution 9.00Å

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