4u4z: Difference between revisions
New page: '''Unreleased structure''' The entry 4u4z is ON HOLD Authors: Garreau de Loubresse, N., Prokhorova, I., Yusupova, G., Yusupov, M. Description: Crystal structure of Phyllanthoside bound... |
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The | ==Crystal structure of Phyllanthoside bound to the yeast 80S ribosome== | ||
<StructureSection load='4u4z' size='340' side='right'caption='[[4u4z]], [[Resolution|resolution]] 3.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4u4z]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ulj 4ulj], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ulk 4ulk], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ulm 4ulm], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4uln 4uln] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ulo 4ulo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U4Z 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]] 3.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3K5:3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2S,3aR,4S,5R,6S,7aS)-5-methyl-4-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3-[1]benzofuran-2,2-pyran]-6-yl]carbonyl}-beta-D-glucopyranose'>3K5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OHX:OSMIUM+(III)+HEXAMMINE'>OHX</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=4u4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u4z OCA], [https://pdbe.org/4u4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u4z RCSB], [https://www.ebi.ac.uk/pdbsum/4u4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u4z ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/STM1_YEAST STM1_YEAST] Binds specifically G4 quadruplex (these are four-stranded right-handed helices, stabilized by guanine base quartets) and purine motif triplex (characterized by a third, antiparallel purine-rich DNA strand located within the major groove of a homopurine stretch of duplex DNA) nucleic acid structures. These structures may be present at telomeres or in rRNAs. Acts with CDC13 to control telomere length homeostasis. Involved in the control of the apoptosis-like cell death.<ref>PMID:15044472</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The ribosome is a molecular machine responsible for protein synthesis and a major target for small-molecule inhibitors. Compared to the wealth of structural information available on ribosome-targeting antibiotics in bacteria, our understanding of the binding mode of ribosome inhibitors in eukaryotes is currently limited. Here we used X-ray crystallography to determine 16 high-resolution structures of 80S ribosomes from Saccharomyces cerevisiae in complexes with 12 eukaryote-specific and 4 broad-spectrum inhibitors. All inhibitors were found associated with messenger RNA and transfer RNA binding sites. In combination with kinetic experiments, the structures suggest a model for the action of cycloheximide and lactimidomycin, which explains why lactimidomycin, the larger compound, specifically targets the first elongation cycle. The study defines common principles of targeting and resistance, provides insights into translation inhibitor mode of action and reveals the structural determinants responsible for species selectivity which could guide future drug development. | |||
Structural basis for the inhibition of the eukaryotic ribosome.,Garreau de Loubresse N, Prokhorova I, Holtkamp W, Rodnina MV, Yusupova G, Yusupov M Nature. 2014 Sep 25;513(7519):517-22. doi: 10.1038/nature13737. Epub 2014 Sep 10. PMID:25209664<ref>PMID:25209664</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4u4z" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribosome 3D structures|Ribosome 3D structures]] | |||
*[[3D sructureseceptor for activated protein kinase C 1|3D sructureseceptor for activated protein kinase C 1]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae S288C]] | |||
[[Category: Garreau de Loubresse N]] | |||
[[Category: Prokhorova I]] | |||
[[Category: Yusupov M]] | |||
[[Category: Yusupova G]] | |||