8pv4 - Revision history

OCA at 12:33, 20 December 2023

2023-12-20T12:33:50Z

←Older revision		Revision as of 12:33, 20 December 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8pv4 is ~~ON HOLD until Paper~~ Publication	+	==Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure==
		+	<StructureSection load='8pv4' size='340' side='right'caption='[[8pv4]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8pv4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PV4 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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=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=8pv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pv4 OCA], [https://pdbe.org/8pv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pv4 RCSB], [https://www.ebi.ac.uk/pdbsum/8pv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pv4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G0S1R0_CHATD G0S1R0_CHATD]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180 degrees rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.

-	~~Authors~~:	+	Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.,Thoms M, Lau B, Cheng J, Fromm L, Denk T, Kellner N, Flemming D, Fischer P, Falquet L, Berninghausen O, Beckmann R, Hurt E EMBO Rep. 2023 Nov 3:e57984. doi: 10.15252/embr.202357984. PMID:37921038<ref>PMID:37921038</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8pv4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chaetomium thermophilum var. thermophilum DSM 1495]]
		+	[[Category: Large Structures]]
		+	[[Category: Beckmann R]]
		+	[[Category: Berninghausen O]]
		+	[[Category: Cheng J]]
		+	[[Category: Denk T]]
		+	[[Category: Thoms M]]

OCA: Replacing page with ''''Unreleased structure''' The entry 8pv4 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures'

2023-11-22T05:38:34Z

Replacing page with ''''Unreleased structure''' The entry 8pv4 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures'

←Older revision		Revision as of 05:38, 22 November 2023
Line 1:		Line 1:
		+	'''Unreleased structure'''

-	~~==Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure==~~	+	The entry 8pv4 is ON HOLD until Paper Publication
-	~~<StructureSection load='~~8pv4~~' size='340' side='right'caption='[[8pv4]], [[Resolution\|resolution]] 2.90Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[8pv4]]~~ is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PV4 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]] 2.9Å</td></tr>~~	+
-	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=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=8pv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pv4 OCA], [https://pdbe.org/8pv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pv4 RCSB], [https://www.ebi.ac.uk/pdbsum/8pv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pv4 ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Function ==~~	+
-	~~[https://www.uniprot.org/uniprot/G0S1R0_CHATD G0S1R0_CHATD]~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	== Publication ~~Abstract from PubMed ==~~	+
-	The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180 degrees rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.	+

-	Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.,Thoms M, Lau B, Cheng J, Fromm L, Denk T, Kellner N, Flemming D, Fischer P, Falquet L, Berninghausen O, Beckmann R, Hurt E EMBO Rep. 2023 Nov 3:~~e57984. doi: 10.15252/embr.202357984. PMID:37921038<ref>PMID:37921038</ref>~~	+	Authors:

-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	Description:
-	~~</div>~~	+	[[Category: Unreleased Structures]]
-	~~<div class="pdbe-citations 8pv4" style="background-color~~:~~#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	[[Category: ~~Chaetomium thermophilum var. thermophilum DSM 1495]]~~	+
-	~~[[Category: Large~~ Structures]]	+
-	~~[[Category: Beckmann R]]~~	+
-	~~[[Category: Berninghausen O]]~~	+
-	~~[[Category: Cheng J]]~~	+
-	~~[[Category: Denk T]]~~	+
-	~~[[Category: Thoms M~~]]	+

OCA at 07:40, 15 November 2023

2023-11-15T07:40:42Z

←Older revision		Revision as of 07:40, 15 November 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8pv4 is ~~ON HOLD until Paper~~ Publication	+	==Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure==
		+	<StructureSection load='8pv4' size='340' side='right'caption='[[8pv4]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8pv4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PV4 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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=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=8pv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pv4 OCA], [https://pdbe.org/8pv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pv4 RCSB], [https://www.ebi.ac.uk/pdbsum/8pv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pv4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G0S1R0_CHATD G0S1R0_CHATD]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180 degrees rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.

-	~~Authors~~:	+	Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.,Thoms M, Lau B, Cheng J, Fromm L, Denk T, Kellner N, Flemming D, Fischer P, Falquet L, Berninghausen O, Beckmann R, Hurt E EMBO Rep. 2023 Nov 3:e57984. doi: 10.15252/embr.202357984. PMID:37921038<ref>PMID:37921038</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8pv4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chaetomium thermophilum var. thermophilum DSM 1495]]
		+	[[Category: Large Structures]]
		+	[[Category: Beckmann R]]
		+	[[Category: Berninghausen O]]
		+	[[Category: Cheng J]]
		+	[[Category: Denk T]]
		+	[[Category: Thoms M]]

OCA at 10:35, 1 November 2023

2023-11-01T10:35:22Z

←Older revision		Revision as of 10:35, 1 November 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8pv4 is ON HOLD	+	The entry 8pv4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8pv4" [edit=sysop:move=sysop]

2023-07-26T11:02:36Z

Protected "8pv4" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:02, 26 July 2023

OCA: New page: '''Unreleased structure''' The entry 8pv4 is ON HOLD Authors: Description: Category: Unreleased Structures

2023-07-26T11:02:32Z

New page: '''Unreleased structure''' The entry 8pv4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8pv4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]