4v7h: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Structure of the 80S rRNA and proteins and P/E tRNA for eukaryotic ribosome based on cryo-EM map of Thermomyces lanuginosus ribosome at 8.9A resolution==
-<StructureSection load='4v7h' size='340' side='right'caption='[[4v7h]], [[Resolution|resolution]] 8.90&Aring;' scene=''>
+<SX load='4v7h' size='340' side='right' viewer='molstar' caption='[[4v7h]], [[Resolution|resolution]] 8.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4v7h]] is a 53 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermomyces_lanuginosus Thermomyces lanuginosus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3jyv 3jyv], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3jyw 3jyw] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3jyx 3jyx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V7H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V7H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4v7h]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermomyces_lanuginosus Thermomyces lanuginosus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3jyv 3jyv], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3jyw 3jyw] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3jyx 3jyx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V7H FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YYG:4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-4,6-DIMETHYL-8-OXO-4,8-DIHYDRO-3H-1,3,4,5,7A-PENTAAZA-S-INDACEN-YLAMINO-BUTYRIC+ACID+METHYL+ESTER'>YYG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 8.9&#8491;</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=4v7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v7h OCA], [http://pdbe.org/4v7h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v7h RCSB], [http://www.ebi.ac.uk/pdbsum/4v7h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v7h ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YYG:4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-4,6-DIMETHYL-8-OXO-4,8-DIHYDRO-3H-1,3,4,5,7A-PENTAAZA-S-INDACEN-YLAMINO-BUTYRIC+ACID+METHYL+ESTER'>YYG</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=4v7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v7h OCA], [https://pdbe.org/4v7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v7h RCSB], [https://www.ebi.ac.uk/pdbsum/4v7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v7h ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in extraribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2.
-Comprehensive molecular structure of the eukaryotic ribosome.,Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J Structure. 2009 Dec 9;17(12):1591-604. PMID:20004163<ref>PMID:20004163</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4v7h" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Receptor for activated protein kinase C 1|Receptor for activated protein kinase C 1]]
 *[[Ribosomal protein L8|Ribosomal protein L8]]
 *[[Ribosomal protein S29|Ribosomal protein S29]]
@@ Line 24: / Line 15: @@
 *[[Ribosome 3D structures|Ribosome 3D structures]]
 *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-== References ==
+*[[3D sructureseceptor for activated protein kinase C 1|3D sructureseceptor for activated protein kinase C 1]]
-<references/>
 __TOC__
-</StructureSection>
+</SX>
 [[Category: Large Structures]]
 [[Category: Thermomyces lanuginosus]]
-[[Category: Devkota, B]]
+[[Category: Devkota B]]
-[[Category: Frank, J]]
+[[Category: Frank J]]
-[[Category: Harvey, S C]]
+[[Category: Harvey SC]]
-[[Category: Huang, A D]]
+[[Category: Huang AD]]
-[[Category: Narayanan, E]]
+[[Category: Narayanan E]]
-[[Category: Sali, A]]
+[[Category: Sali A]]
-[[Category: Taylor, D J]]
+[[Category: Taylor DJ]]
-[[Category: Topf, M]]
+[[Category: Topf M]]
-[[Category: Eukaryotic ribosome]]
-[[Category: Flexible fitting]]
-[[Category: Rack1 protein]]
-[[Category: Ribosome]]