3iyy: Difference between revisions

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<SX load='3iyy' size='340' side='right' viewer='molstar' caption='[[3iyy]], [[Resolution|resolution]] 10.90&Aring;' scene=''>
<SX load='3iyy' size='340' side='right' viewer='molstar' caption='[[3iyy]], [[Resolution|resolution]] 10.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3iyy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYY FirstGlance]. <br>
<table><tr><td colspan='2'>[[3iyy]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O55:H7_str._CB9615 Escherichia coli O55:H7 str. CB9615]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYY FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2aw7|2aw7]], [[2awb|2awb]], [[2wrj|2wrj]]</div></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]] 10.9&#8491;</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=3iyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyy OCA], [https://pdbe.org/3iyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iyy RCSB], [https://www.ebi.ac.uk/pdbsum/3iyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyy ProSAT]</span></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=3iyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyy OCA], [https://pdbe.org/3iyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iyy RCSB], [https://www.ebi.ac.uk/pdbsum/3iyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyy ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/D3QYD6_ECOCB D3QYD6_ECOCB]] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501][SAAS:SAAS027491_004_000769] [[https://www.uniprot.org/uniprot/D3QTD7_ECOCB D3QTD7_ECOCB]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity).[HAMAP-Rule:MF_01315] [[https://www.uniprot.org/uniprot/D3QTE7_ECOCB D3QTE7_ECOCB]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs (By similarity).[HAMAP-Rule:MF_01333]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iyy ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iyy ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The ribosomal intersubunit bridges maintain the overall architecture of the ribosome and thereby play a pivotal role in the dynamics of translation. The only protein-protein bridge, b1b, is formed by the two proteins, S13 and L5 of the small and large ribosomal subunits, respectively. B1b absorbs the largest movement during ratchet-like motion, and its two proteins reorganize in different constellations during this motion of the ribosome. Our results in this study of b1b in the Escherichia coli 70S ribosome suggest that the intrinsic molecular features of the bridging proteins allow the bridge to modulate the ratchet-like motion in a controlled manner. Additionally, another large subunit protein, L31, seems to participate with S13 and L5 in the formation, dynamics, and stabilization of this bridge.
Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome.,Shasmal M, Chakraborty B, Sengupta J Biochem Biophys Res Commun. 2010 Aug 20;399(2):192-197. Epub 2010 Jul 17. PMID:20643101<ref>PMID:20643101</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3iyy" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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*[[Ribosomal protein L5|Ribosomal protein L5]]
*[[Ribosomal protein L5|Ribosomal protein L5]]
*[[Ribosomal protein S13|Ribosomal protein S13]]
*[[Ribosomal protein S13|Ribosomal protein S13]]
== References ==
<references/>
__TOC__
__TOC__
</SX>
</SX>
[[Category: Escherichia coli]]
[[Category: Escherichia coli O55:H7 str. CB9615]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chakraborty, B]]
[[Category: Chakraborty B]]
[[Category: Sengupta, J]]
[[Category: Sengupta J]]
[[Category: Shasmal, M]]
[[Category: Shasmal M]]
[[Category: B1b bridge]]
[[Category: Ratchet-like motion]]
[[Category: Ribosomal intersubunit bridge]]
[[Category: Ribosomal protein]]
[[Category: Ribosomal protein l31]]
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