3ep2

From Proteopedia

(Difference between revisions)

Revision as of 23:26, 4 August 2016

Model 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 Ecoli and Escherichia coli k12. 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, PDBe, RCSB, PDBsum, ProSAT

Function

[RL11_ECOLI] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [RS12_ECOLI] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] Cryo-EM studies suggest that S12 contacts the EF-Tu bound tRNA in the A-site during codon-recognition. This contact is most likely broken as the aminoacyl-tRNA moves into the peptidyl transferase center in the 50S subunit.[HAMAP-Rule:MF_00403_B]

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.

References

↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ep2"

@@ Line 1: / Line 1: @@
 ==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>
+<table><tr><td colspan='2'>[[3ep2]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. 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 id='related'><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 id='resources'><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>
+<tr id='resources'><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://pdbe.org/3ep2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ep2 RCSB], [http://www.ebi.ac.uk/pdbsum/3ep2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ep2 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 16: / Line 17: @@
     <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].
+</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=3ep2 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3ep2" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Elongation factor|Elongation factor]]
+*[[Ribosomal protein L11|Ribosomal protein L11]]
+*[[Ribosomal protein S12|Ribosomal protein S12]]
+*[[TRNA|TRNA]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli k-12]]
+[[Category: Ecoli]]
+[[Category: Escherichia coli k12]]
 [[Category: Agirrezabala, X]]
 [[Category: Frank, J]]

3ep2

From Proteopedia

Revision as of 23:26, 4 August 2016

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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