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3jbs

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Current revision (08:43, 7 February 2024) (edit) (undo)
 
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<SX load='3jbs' size='340' side='right' viewer='molstar' caption='[[3jbs]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<SX load='3jbs' size='340' side='right' viewer='molstar' caption='[[3jbs]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3jbs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_by4741 Saccharomyces cerevisiae by4741]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JBS FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3jbs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_BY4741 Saccharomyces cerevisiae BY4741]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JBS FirstGlance]. <br>
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</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=3jbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbs OCA], [https://pdbe.org/3jbs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jbs RCSB], [https://www.ebi.ac.uk/pdbsum/3jbs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbs ProSAT]</span></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3jbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbs OCA], [https://pdbe.org/3jbs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jbs RCSB], [https://www.ebi.ac.uk/pdbsum/3jbs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbs ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/RL6A_YEAST RL6A_YEAST]
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A single-particle cryoEM reconstruction of the large ribosomal subunit from Saccharomyces cerevisiae was obtained from a dataset of approximately 75,000 particles. The gold-standard and frequency-limited approaches to single-particle refinement were each independently used to determine orientation parameters for the final reconstruction. Both approaches showed similar resolution curves and nominal resolution values for the 60S dataset, estimated at 2.9A. The amount of over-fitting present during frequency-limited refinement was quantitatively analyzed using the high-resolution phase-randomization test, and the results showed no apparent over-fitting. The number of asymmetric subunits required to reach specific resolutions was subsequently analyzed by refining subsets of the data in an ab initio manner. With our data collection and processing strategies, sub-nanometer resolution was obtained with approximately 200 asymmetric subunits (or, equivalently for the ribosomal subunit, particles). Resolutions of 5.6A, 4.5A, and 3.8A were reached with approximately 1000, approximately 1600, and approximately 5000 asymmetric subunits, respectively. At these resolutions, one would expect to detect alpha-helical pitch, separation of beta-strands, and separation of Calpha atoms, respectively. Using this map, together with strategies for ab initio model building and model refinement, we built a region of the ribosomal protein eL6, which was missing in previous models of the yeast ribosome. The relevance for more routine high-resolution structure determination is discussed.
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Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits.,Passos DO, Lyumkis D J Struct Biol. 2015 Nov;192(2):235-44. doi: 10.1016/j.jsb.2015.10.002. Epub 2015 , Oct 22. PMID:26470814<ref>PMID:26470814</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3jbs" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</SX>
</SX>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Saccharomyces cerevisiae by4741]]
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[[Category: Saccharomyces cerevisiae BY4741]]
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[[Category: Lyumkis, D]]
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[[Category: Lyumkis D]]
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[[Category: Passos, D O]]
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[[Category: Passos DO]]
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[[Category: Ribosome]]
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[[Category: Translation]]
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Current revision

eL6 protein from yeast 60S ribosomal subunit

3jbs, resolution 2.90Å

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