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| - | [[Image:2oe5.gif|left|200px]] | |
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| - | {{Structure
| + | ==1.5 A X-ray crystal structure of Apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding A site: RNA construct with 3'-overhang== |
| - | |PDB= 2oe5 |SIZE=350|CAPTION= <scene name='initialview01'>2oe5</scene>, resolution 1.51Å
| + | <StructureSection load='2oe5' size='340' side='right'caption='[[2oe5]], [[Resolution|resolution]] 1.51Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[2oe5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OE5 FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.51Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2oe5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oe5 OCA], [https://pdbe.org/2oe5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oe5 RCSB], [https://www.ebi.ac.uk/pdbsum/2oe5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oe5 ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[2oe6|2OE6]], [[2oe8|2OE8]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oe5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oe5 OCA], [http://www.ebi.ac.uk/pdbsum/2oe5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2oe5 RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''1.5 A X-ray crystal structure of Apramycin complex with RNA fragment GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC containing the human ribosomal decoding A site: RNA construct with 3'-overhang'''
| + | [[Category: Hermann T]] |
| - | | + | [[Category: Patel DJ]] |
| - | | + | [[Category: Skripkin E]] |
| - | ==Overview==
| + | [[Category: Tereshko V]] |
| - | Aminoglycoside antibiotics bind specifically to the bacterial ribosomal decoding-site RNA and thereby interfere with fidelity but not efficiency of translation. Apramycin stands out among aminoglycosides for its mechanism of action which is based on blocking translocation and its ability to bind also to the eukaryotic decoding site despite differences in key residues required for apramycin recognition by the bacterial target. To elucidate molecular recognition of the eukaryotic decoding site by apramycin we have determined the crystal structure of an oligoribonucleotide containing the human sequence free and in complex with the antibiotic at 1.5 A resolution. The drug binds in the deep groove of the RNA which forms a continuously stacked helix comprising non-canonical C.A and G.A base pairs and a bulged-out adenine. The binding mode of apramycin at the human decoding-site RNA is distinct from aminoglycoside recognition of the bacterial target, suggesting a molecular basis for the actions of apramycin in eukaryotes and bacteria.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 2OE5 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OE5 OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Apramycin recognition by the human ribosomal decoding site., Hermann T, Tereshko V, Skripkin E, Patel DJ, Blood Cells Mol Dis. 2007 May-Jun;38(3):193-8. Epub 2007 Jan 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17258916 17258916]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Hermann, T.]] | + | |
| - | [[Category: Patel, D J.]] | + | |
| - | [[Category: Skripkin, E.]] | + | |
| - | [[Category: Tereshko, V.]] | + | |
| - | [[Category: a site]]
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| - | [[Category: aminoglycoside antibiotic]]
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| - | [[Category: apramycin]]
| + | |
| - | [[Category: homo sapien]]
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| - | [[Category: ribosomal decoding site]]
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| - | [[Category: rna duplex]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:16:28 2008''
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