4u3u

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Cycloheximide bound to the yeast 80S ribosome

Structural highlights

4u3u is a 20 chain structure with sequence from Saccharomyces cerevisiae S288C. This structure supersedes the now removed PDB entries 4uk9, 4uka, 4ukb, 4ukc and 4uke. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RSSA1_YEAST Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits.^[1] ^[2]

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^[3]

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

References

↑ Ford CL, Randal-Whitis L, Ellis SR. Yeast proteins related to the p40/laminin receptor precursor are required for 20S ribosomal RNA processing and the maturation of 40S ribosomal subunits. Cancer Res. 1999 Feb 1;59(3):704-10. PMID:9973221
↑ Tabb-Massey A, Caffrey JM, Logsden P, Taylor S, Trent JO, Ellis SR. Ribosomal proteins Rps0 and Rps21 of Saccharomyces cerevisiae have overlapping functions in the maturation of the 3' end of 18S rRNA. Nucleic Acids Res. 2003 Dec 1;31(23):6798-805. PMID:14627813
↑ Garreau de Loubresse N, Prokhorova I, Holtkamp W, Rodnina MV, Yusupova G, Yusupov M. Structural basis for the inhibition of the eukaryotic ribosome. Nature. 2014 Sep 25;513(7519):517-22. doi: 10.1038/nature13737. Epub 2014 Sep 10. PMID:25209664 doi:http://dx.doi.org/10.1038/nature13737

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4u3u"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Cycloheximide bound to the yeast 80S ribosome==
-<StructureSection load='4u3u' size='340' side='right' caption='[[4u3u]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='4u3u' size='340' side='right'caption='[[4u3u]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4u3u]] is a 162 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_atcc_204508_/_s288c Saccharomyces cerevisiae atcc 204508 / s288c]. This structure supersedes the now removed PDB entries  and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4uke 4uke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U3U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4u3u]] 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=4uk9 4uk9], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4uka 4uka], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ukb 4ukb], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ukc 4ukc] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4uke 4uke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U3U FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HE:4-{(2R)-2-[(1S,3S,5S)-3,5-DIMETHYL-2-OXOCYCLOHEXYL]-2-HYDROXYETHYL}PIPERIDINE-2,6-DIONE'>3HE</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3HE:4-{(2R)-2-[(1S,3S,5S)-3,5-DIMETHYL-2-OXOCYCLOHEXYL]-2-HYDROXYETHYL}PIPERIDINE-2,6-DIONE'>3HE</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4uk9|4uk9]], [[4uka|4uka]], [[4ukb|4ukb]], [[4ukc|4ukc]], [[4uke|4uke]]</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=4u3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u3u OCA], [https://pdbe.org/4u3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u3u RCSB], [https://www.ebi.ac.uk/pdbsum/4u3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u3u ProSAT]</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=4u3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u3u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u3u RCSB], [http://www.ebi.ac.uk/pdbsum/4u3u PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RSSA1_YEAST RSSA1_YEAST] Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits.<ref>PMID:9973221</ref> <ref>PMID:14627813</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4u3u" 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: Saccharomyces cerevisiae atcc 204508 / s288c]]
+[[Category: Large Structures]]
-[[Category: Loubresse, N Garreau de]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Prokhorova, I]]
+[[Category: Garreau de Loubresse N]]
-[[Category: Yusupov, M]]
+[[Category: Prokhorova I]]
-[[Category: Yusupova, G]]
+[[Category: Yusupov M]]
-[[Category: Antibiotic]]
+[[Category: Yusupova G]]
-[[Category: Eukaryote]]
-[[Category: Inhibitor]]
-[[Category: Ribosome]]
-[[Category: Rna-protein complex]]
-[[Category: Translation]]

4u3u

From Proteopedia

Current revision

Crystal structure of Cycloheximide bound to the yeast 80S ribosome

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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