7sa4 - Revision history

OCA at 03:15, 8 September 2022

OCA — Thu, 08 Sep 2022 03:15:49 GMT

←Older revision		Revision as of 03:15, 8 September 2022
Line 1:		Line 1:

-	====	+	==Damaged 70S ribosome with PrfH bound==
-	<StructureSection load='7sa4' size='340' side='right'caption='[[7sa4]]' scene=''>	+	<StructureSection load='7sa4' size='340' side='right'caption='[[7sa4]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7sa4]] is a 11 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=7SA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SA4 FirstGlance]. <br>
-	</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=7sa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sa4 OCA], [https://pdbe.org/7sa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sa4 RCSB], [https://www.ebi.ac.uk/pdbsum/7sa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sa4 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <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=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=A3P:ADENOSINE-3-5-DIPHOSPHATE'>A3P</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</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=7sa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sa4 OCA], [https://pdbe.org/7sa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sa4 RCSB], [https://www.ebi.ac.uk/pdbsum/7sa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sa4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A0J2A6L0_ECOLX A0A0J2A6L0_ECOLX]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RtcB is involved in transfer RNA (tRNA) splicing in archaeal and eukaryotic organisms. However, most RtcBs are found in bacteria, whose tRNAs have no introns. Because tRNAs are the substrates of archaeal and eukaryotic RtcB, it is assumed that bacterial RtcBs are for repair of damaged tRNAs. Here, we show that a subset of bacterial RtcB, denoted RtcB2 herein, specifically repair ribosomal damage in the decoding center. To access the damage site for repair, however, the damaged 70S ribosome needs to be dismantled first, and this is accomplished by bacterial PrfH. Peptide-release assays revealed that PrfH is only active with the damaged 70S ribosome but not with the intact one. A 2.55-A cryo-electron microscopy structure of PrfH in complex with the damaged 70S ribosome provides molecular insight into PrfH discriminating between the damaged and the intact ribosomes via specific recognition of the cleaved 3'-terminal nucleotide. RNA repair assays demonstrated that RtcB2 efficiently repairs the damaged 30S ribosomal subunit but not the damaged tRNAs. Cell-based assays showed that the RtcB2-PrfH pair reverse the damage inflicted by ribosome-specific ribotoxins in vivo. Thus, our combined biochemical, structural, and cell-based studies have uncovered a bacterial defense system specifically evolved to reverse the lethal ribosomal damage in the decoding center for cell survival.
		+
		+	Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB.,Tian Y, Zeng F, Raybarman A, Fatma S, Carruthers A, Li Q, Huang RH Proc Natl Acad Sci U S A. 2022 Jul 19;119(29):e2202464119. doi:, 10.1073/pnas.2202464119. Epub 2022 Jul 12. PMID:35858322<ref>PMID:35858322</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7sa4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Carruthers A]]
		+	[[Category: Fatma S]]
		+	[[Category: Huang RH]]
		+	[[Category: Li Q]]
		+	[[Category: Raybarman A]]
		+	[[Category: Tian Y]]
		+	[[Category: Zeng F]]

OCA at 04:53, 3 August 2022

OCA — Wed, 03 Aug 2022 04:53:01 GMT

←Older revision		Revision as of 04:53, 3 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7sa4 ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7sa4' size='340' side='right'caption='[[7sa4]]' scene=''>
-	~~Authors~~: ~~Tian, Y~~.~~, Zeng, F~~.~~, Raybarman, A~~.~~, Carruthers, A~~.~~, Li, Q~~.~~, Fatma, S~~.~~, Huang, R.H~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Damaged 70S ribosome with PrfH bound~~	+	</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=7sa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sa4 OCA], [https://pdbe.org/7sa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sa4 RCSB], [https://www.ebi.ac.uk/pdbsum/7sa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sa4 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~Raybarman~~, ~~A]]~~	+	__TOC__
-	[~~[Category~~: ~~Zeng, F~~]]	+	</StructureSection>
-	[~~[Category~~: ~~Huang, R~~.H]]	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Fatma~~, ~~S]]~~	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Tian, Y]~~]	+
-	[[Category: ~~Carruthers, A~~]]	+
-	[[Category: ~~Li, Q~~]]	+

OCA at 04:13, 6 October 2021

OCA — Wed, 06 Oct 2021 04:13:43 GMT

←Older revision		Revision as of 04:13, 6 October 2021
Line 3:		Line 3:
	The entry 7sa4 is ON HOLD		The entry 7sa4 is ON HOLD

-	Authors: Tian, Y., Zeng, F., Raybarman, A., Carruthers, A., Li, Q., Fatma, s., Huang, R.H.	+	Authors: Tian, Y., Zeng, F., Raybarman, A., Carruthers, A., Li, Q., Fatma, S., Huang, R.H.

	Description: Damaged 70S ribosome with PrfH bound		Description: Damaged 70S ribosome with PrfH bound
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Raybarman, A]]
	[[Category: Zeng, F]]		[[Category: Zeng, F]]
	[[Category: Huang, R.H]]		[[Category: Huang, R.H]]
		+	[[Category: Fatma, S]]
	[[Category: Tian, Y]]		[[Category: Tian, Y]]
	[[Category: Carruthers, A]]		[[Category: Carruthers, A]]
-	[[Category: Raybarman, A]]
-	[[Category: Fatma, S]]
	[[Category: Li, Q]]		[[Category: Li, Q]]

OCA: Protected "7sa4" [edit=sysop:move=sysop]

OCA — Wed, 29 Sep 2021 07:49:44 GMT

Protected "7sa4" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:49, 29 September 2021

OCA: New page: '''Unreleased structure''' The entry 7sa4 is ON HOLD Authors: Tian, Y., Zeng, F., Raybarman, A., Carruthers, A., Li, Q., Fatma, s., Huang, R.H. Description: Damaged 70S ribosome with P...

OCA — Wed, 29 Sep 2021 07:49:43 GMT

New page: '''Unreleased structure''' The entry 7sa4 is ON HOLD Authors: Tian, Y., Zeng, F., Raybarman, A., Carruthers, A., Li, Q., Fatma, s., Huang, R.H. Description: Damaged 70S ribosome with P...

New page

'''Unreleased structure'''

The entry 7sa4 is ON HOLD

Authors: Tian, Y., Zeng, F., Raybarman, A., Carruthers, A., Li, Q., Fatma, s., Huang, R.H.

Description: Damaged 70S ribosome with PrfH bound
[[Category: Unreleased Structures]]
[[Category: Zeng, F]]
[[Category: Huang, R.H]]
[[Category: Tian, Y]]
[[Category: Carruthers, A]]
[[Category: Raybarman, A]]
[[Category: Fatma, S]]
[[Category: Li, Q]]