4tue: Difference between revisions

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'''Unreleased structure'''


The entry 4tue is ON HOLD
==Crystal structure of ASL-SufJ bound to Codon ACC-U on the Ribosome==
<StructureSection load='4tue' size='340' side='right'caption='[[4tue]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4tue]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TUE FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=PPU:PUROMYCIN-5-MONOPHOSPHATE'>PPU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4tue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tue OCA], [https://pdbe.org/4tue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tue RCSB], [https://www.ebi.ac.uk/pdbsum/4tue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tue ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-nucleotide mRNA reading frame is tightly regulated during translation to ensure accurate protein expression. Translation errors that lead to aberrant protein production can result from the uncoupled movement of the tRNA in either the 5' or 3' direction on mRNA. Here, we report the biochemical and structural characterization of +1 frameshift suppressor tRNA(SufJ), a tRNA known to decode four, instead of three, nucleotides. Frameshift suppressor tRNA(SufJ) contains an insertion 5' to its anticodon, expanding the anticodon loop from seven to eight nucleotides. Our results indicate that the expansion of the anticodon loop of either ASL(SufJ) or tRNA(SufJ) does not affect its affinity for the A site of the ribosome. Structural analyses of both ASL(SufJ) and ASL(Thr) bound to the Thermus thermophilus 70S ribosome demonstrate both ASLs decode in the zero frame. Although the anticodon loop residues 34-37 are superimposable with canonical seven-nucleotide ASLs, the single C31.5 insertion between nucleotides 31 and 32 in ASL(SufJ) imposes a conformational change of the anticodon stem, that repositions and tilts the ASL toward the back of the A site. Further modeling analyses reveal that this tilting would cause a distortion in full-length A-site tRNA(SufJ) during tRNA selection and possibly impede gripping of the anticodon stem by 16S rRNA nucleotides in the P site. Together, these data implicate tRNA distortion as a major driver of noncanonical translation events such as frameshifting.


Authors: Fagan, C.E., Dunham, C.M.
Structural insights into translational recoding by frameshift suppressor tRNASufJ.,Fagan CE, Maehigashi T, Dunkle JA, Miles SJ, Dunham CM RNA. 2014 Dec;20(12):1944-54. doi: 10.1261/rna.046953.114. Epub 2014 Oct 28. PMID:25352689<ref>PMID:25352689</ref>


Description: Crystal structure of ASL-SufJ bound to Codon ACC-U on the Ribosome
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4tue" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus HB8]]
[[Category: Dunham CM]]
[[Category: Fagan CE]]

Latest revision as of 03:47, 28 December 2023

Crystal structure of ASL-SufJ bound to Codon ACC-U on the RibosomeCrystal structure of ASL-SufJ bound to Codon ACC-U on the Ribosome

Structural highlights

4tue is a 20 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.5Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS2_THET8 Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]

Publication Abstract from PubMed

The three-nucleotide mRNA reading frame is tightly regulated during translation to ensure accurate protein expression. Translation errors that lead to aberrant protein production can result from the uncoupled movement of the tRNA in either the 5' or 3' direction on mRNA. Here, we report the biochemical and structural characterization of +1 frameshift suppressor tRNA(SufJ), a tRNA known to decode four, instead of three, nucleotides. Frameshift suppressor tRNA(SufJ) contains an insertion 5' to its anticodon, expanding the anticodon loop from seven to eight nucleotides. Our results indicate that the expansion of the anticodon loop of either ASL(SufJ) or tRNA(SufJ) does not affect its affinity for the A site of the ribosome. Structural analyses of both ASL(SufJ) and ASL(Thr) bound to the Thermus thermophilus 70S ribosome demonstrate both ASLs decode in the zero frame. Although the anticodon loop residues 34-37 are superimposable with canonical seven-nucleotide ASLs, the single C31.5 insertion between nucleotides 31 and 32 in ASL(SufJ) imposes a conformational change of the anticodon stem, that repositions and tilts the ASL toward the back of the A site. Further modeling analyses reveal that this tilting would cause a distortion in full-length A-site tRNA(SufJ) during tRNA selection and possibly impede gripping of the anticodon stem by 16S rRNA nucleotides in the P site. Together, these data implicate tRNA distortion as a major driver of noncanonical translation events such as frameshifting.

Structural insights into translational recoding by frameshift suppressor tRNASufJ.,Fagan CE, Maehigashi T, Dunkle JA, Miles SJ, Dunham CM RNA. 2014 Dec;20(12):1944-54. doi: 10.1261/rna.046953.114. Epub 2014 Oct 28. PMID:25352689[1]

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

See Also

References

  1. Fagan CE, Maehigashi T, Dunkle JA, Miles SJ, Dunham CM. Structural insights into translational recoding by frameshift suppressor tRNASufJ. RNA. 2014 Dec;20(12):1944-54. doi: 10.1261/rna.046953.114. Epub 2014 Oct 28. PMID:25352689 doi:http://dx.doi.org/10.1261/rna.046953.114

4tue, resolution 3.50Å

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