6ot3: Difference between revisions

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-'''Unreleased structure'''
-The entry 6ot3 is ON HOLD
+==RF2 accommodated state bound Release complex 70S at 24 ms==
+<SX load='6ot3' size='340' side='right' viewer='molstar' caption='[[6ot3]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6ot3]] is a 10 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=6OT3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OT3 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6ot3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ot3 OCA], [https://pdbe.org/6ot3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ot3 RCSB], [https://www.ebi.ac.uk/pdbsum/6ot3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ot3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL35_ECOLI RL35_ECOLI]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 A away. Surprisingly, free RF2 is compact, with only 20 A between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 A resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.
-Authors: Fu, Z., Indrisiunaite, G., Kaledhonkar, S., Shah, B., Sun, M., Chen, B., Grassucci, R.A., Ehrenberg, M., Frank, J.
+The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.,Fu Z, Indrisiunaite G, Kaledhonkar S, Shah B, Sun M, Chen B, Grassucci RA, Ehrenberg M, Frank J Nat Commun. 2019 Jun 12;10(1):2579. doi: 10.1038/s41467-019-10608-z. PMID:31189921<ref>PMID:31189921</ref>
-Description: RF2 accommodated state bound Release complex 70S at 24 ms
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Ehrenberg, M]]
+<div class="pdbe-citations 6ot3" style="background-color:#fffaf0;"></div>
-[[Category: Fu, Z]]
-[[Category: Frank, J]]
+==See Also==
-[[Category: Kaledhonkar, S]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-[[Category: Sun, M]]
+== References ==
-[[Category: Indrisiunaite, G]]
+<references/>
-[[Category: Grassucci, R.A]]
+__TOC__
-[[Category: Shah, B]]
+</SX>
-[[Category: Chen, B]]
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Chen B]]
+[[Category: Ehrenberg M]]
+[[Category: Frank J]]
+[[Category: Fu Z]]
+[[Category: Grassucci RA]]
+[[Category: Indrisiunaite G]]
+[[Category: Kaledhonkar S]]
+[[Category: Shah B]]
+[[Category: Sun M]]