3iz4: Difference between revisions

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==Modified E. coli tmRNA in the resume state with the tRNA-like domain in the ribosomal P site interacting with the SmpB==
==Modified E. coli tmRNA in the resume state with the tRNA-like domain in the ribosomal P site interacting with the SmpB==
<StructureSection load='3iz4' size='340' side='right' caption='[[3iz4]], [[Resolution|resolution]] 13.60&Aring;' scene=''>
<SX load='3iz4' size='340' side='right' viewer='molstar' caption='[[3iz4]], [[Resolution|resolution]] 13.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3iz4]] is a 2 chain structure with 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=3IZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IZ4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3iz4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The January 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Transfer-Messenger RNA''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_1 10.2210/rcsb_pdb/mom_2013_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IZ4 FirstGlance]. <br>
</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=3iz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iz4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iz4 RCSB], [http://www.ebi.ac.uk/pdbsum/3iz4 PDBsum]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 13.6&#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=3iz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iz4 OCA], [https://pdbe.org/3iz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iz4 RCSB], [https://www.ebi.ac.uk/pdbsum/3iz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iz4 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/SSRP_THET8 SSRP_THET8] Binds specifically to the SsrA RNA (tmRNA) and is required for stable association of SsrA with ribosomes (By similarity).
Bacterial ribosomes stalled by truncated mRNAs are rescued by transfer-messenger RNA (tmRNA), a dual-function molecule that contains a tRNA-like domain (TLD) and an internal open reading frame (ORF). Occupying the empty A site with its TLD, the tmRNA enters the ribosome with the help of elongation factor Tu and a protein factor called small protein B (SmpB), and switches the translation to its own ORF. In this study, using cryo-electron microscopy, we obtained the first structure of an in vivo-formed complex containing ribosome and the tmRNA at the point where the TLD is accommodated into the ribosomal P site. We show that tmRNA maintains a stable 'arc and fork' structure on the ribosome when its TLD moves to the ribosomal P site and translation resumes on its ORF. Based on the density map, we built an atomic model, which suggests that SmpB interacts with the five nucleotides immediately upstream of the resume codon, thereby determining the correct selection of the reading frame on the ORF of tmRNA.
 
Visualizing the transfer-messenger RNA as the ribosome resumes translation.,Fu J, Hashem Y, Wower I, Lei J, Liao HY, Zwieb C, Wower J, Frank J EMBO J. 2010 Nov 17;29(22):3819-25. Epub 2010 Oct 12. PMID:20940705<ref>PMID:20940705</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</SX>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Frank, J]]
[[Category: Large Structures]]
[[Category: Fu, J]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Hashem, Y]]
[[Category: Transfer-Messenger RNA]]
[[Category: Molecular mimicry]]
[[Category: Frank J]]
[[Category: Mrna-like domain]]
[[Category: Fu J]]
[[Category: Ms2]]
[[Category: Hashem Y]]
[[Category: Pseudo-knot]]
[[Category: Rna]]
[[Category: Rna binding protein-rna complex]]
[[Category: Trans-translation]]
[[Category: Transfer-messenger rna]]
[[Category: Trna-like domain]]

Latest revision as of 13:08, 21 February 2024

Modified E. coli tmRNA in the resume state with the tRNA-like domain in the ribosomal P site interacting with the SmpBModified E. coli tmRNA in the resume state with the tRNA-like domain in the ribosomal P site interacting with the SmpB

3iz4, resolution 13.60Å

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