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4u56

From Proteopedia

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Current revision

Crystal structure of Blasticidin S bound to the yeast 80S ribosome

Structural highlights

4u56 is a 20 chain structure with sequence from Saccharomyces cerevisiae S288C. This structure supersedes the now removed PDB entries 4ukf, 4ukg, 4ukh, 4uki and 4ukj. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.45Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS15_YEAST Involved in the nuclear export of the small ribosomal subunit. Has a role in the late stage of the assembly of pre-40S particles within the nucleus and controls their export to the cytoplasm.^[1]

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^[2]

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

References

↑ Leger-Silvestre I, Milkereit P, Ferreira-Cerca S, Saveanu C, Rousselle JC, Choesmel V, Guinefoleau C, Gas N, Gleizes PE. The ribosomal protein Rps15p is required for nuclear exit of the 40S subunit precursors in yeast. EMBO J. 2004 Jun 16;23(12):2336-47. Epub 2004 May 27. PMID:15167894 doi:http://dx.doi.org/10.1038/sj.emboj.7600252
↑ 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/4u56"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Blasticidin S bound to the yeast 80S ribosome==
-<StructureSection load='4u56' size='340' side='right' caption='[[4u56]], [[Resolution|resolution]] 3.45&Aring;' scene=''>
+<StructureSection load='4u56' size='340' side='right'caption='[[4u56]], [[Resolution|resolution]] 3.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4u56]] 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=4ukj 4ukj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U56 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4u56]] 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=4ukf 4ukf], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ukg 4ukg], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ukh 4ukh], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4uki 4uki] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ukj 4ukj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U56 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLS:BLASTICIDIN+S'>BLS</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]] 3.45&#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=BLS:BLASTICIDIN+S'>BLS</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">[[4ukf|4ukf]], [[4ukg|4ukg]], [[4ukh|4ukh]], [[4uki|4uki]], [[4ukj|4ukj]]</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=4u56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u56 OCA], [https://pdbe.org/4u56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u56 RCSB], [https://www.ebi.ac.uk/pdbsum/4u56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u56 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=4u56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u56 RCSB], [http://www.ebi.ac.uk/pdbsum/4u56 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS15_YEAST RS15_YEAST] Involved in the nuclear export of the small ribosomal subunit. Has a role in the late stage of the assembly of pre-40S particles within the nucleus and controls their export to the cytoplasm.<ref>PMID:15167894</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 4u56" 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]]

4u56

From Proteopedia

Current revision

Crystal structure of Blasticidin S bound to the yeast 80S ribosome

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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