6p5j - Revision history

OCA at 09:25, 20 March 2024

OCA — Wed, 20 Mar 2024 09:25:47 GMT

←Older revision		Revision as of 09:25, 20 March 2024
Line 3:		Line 3:
	<SX load='6p5j' size='340' side='right' viewer='molstar' caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>		<SX load='6p5j' size='340' side='right' viewer='molstar' caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p5j]] is a 81 chain structure with sequence from [~~http://en.wikipedia.org/wiki/ ] and [http~~://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6P5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p5j]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P5J FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6p4g\|6p4g]]~~, [[~~6p4h~~\|~~6p4h]], [[6p5i\|6p5i~~]]</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]] 3.1Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6p5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5j OCA], [~~http~~://pdbe.org/6p5j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p5j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p5j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5j 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=6p5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5j OCA], [https://pdbe.org/6p5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p5j RCSB], [https://www.ebi.ac.uk/pdbsum/6p5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~U3KPD5_RABIT U3KPD5_RABIT~~]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/G1SS70_RABIT G1SS70_RABIT]] May play a role during erythropoiesis through regulation of transcription factor DDIT3.[HAMAP-Rule:MF_03122]	+	[https://www.uniprot.org/uniprot/G1SP51_RABIT G1SP51_RABIT]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.	+
-		+
-	The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.,Acosta-Reyes F, Neupane R, Frank J, Fernandez IS EMBO J. 2019 Oct 14:e102226. doi: 10.15252/embj.2019102226. PMID:31609474<ref>PMID:31609474</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6p5j" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Ribosome 3D structures\|Ribosome 3D structures]]		*[[Ribosome 3D structures\|Ribosome 3D structures]]
-	~~== References ==~~	+	*[[3D sructureseceptor for activated protein kinase C 1\|3D sructureseceptor for activated protein kinase C 1]]
-	~~<references/>~~	+
	__TOC__		__TOC__
	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Oryctolagus cuniculus]]		[[Category: Oryctolagus cuniculus]]
-	[[Category: Acosta-Reyes~~, F J~~]]	+	[[Category: Acosta-Reyes FJ]]
-	[[Category: Fernandez~~, I S~~]]	+	[[Category: Fernandez IS]]
-	[[Category: Frank, J]]	+	[[Category: Frank J]]
-	[[Category: Neupane, R]]	+	[[Category: Neupane R]]
-	~~[[Category: Internal ribosome entry site]]~~	+
-	~~[[Category: Ire]]~~	+
-	~~[[Category: Israeli acute paralysis virus]]~~	+
-	~~[[Category: Large ribosomal subunit]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Small ribosomal subunit~~]]	+

OCA at 04:20, 11 April 2020

OCA — Sat, 11 Apr 2020 04:20:49 GMT

←Older revision		Revision as of 04:20, 11 April 2020
Line 3:		Line 3:
	<SX load='6p5j' size='340' side='right' viewer='molstar' caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>		<SX load='6p5j' size='340' side='right' viewer='molstar' caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p5j]] is a 81 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p5j]] is a 81 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6P5J FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6p4g\|6p4g]], [[6p4h\|6p4h]], [[6p5i\|6p5i]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6p4g\|6p4g]], [[6p4h\|6p4h]], [[6p5i\|6p5i]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6p5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5j OCA], [http://pdbe.org/6p5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p5j RCSB], [http://www.ebi.ac.uk/pdbsum/6p5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5j ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6p5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5j OCA], [http://pdbe.org/6p5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p5j RCSB], [http://www.ebi.ac.uk/pdbsum/6p5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 23:20, 6 March 2020

OCA — Fri, 06 Mar 2020 23:20:57 GMT

←Older revision		Revision as of 23:20, 6 March 2020
Line 1:		Line 1:

	==Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)==		==Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)==
-	<~~StructureSection~~ load='6p5j' size='340' side='right'caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<SX load='6p5j' size='340' side='right' viewer='molstar' caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6p5j]] is a 81 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P5J FirstGlance]. <br>		<table><tr><td colspan='2'>[[6p5j]] is a 81 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P5J FirstGlance]. <br>
Line 24:		Line 24:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Oryctolagus cuniculus]]		[[Category: Oryctolagus cuniculus]]

OCA at 10:26, 26 February 2020

OCA — Wed, 26 Feb 2020 10:26:16 GMT

←Older revision		Revision as of 10:26, 26 February 2020
Line 3:		Line 3:
	<StructureSection load='6p5j' size='340' side='right'caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6p5j' size='340' side='right'caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p5j]] is a 81 chain structure with sequence from [http://en.wikipedia.org/wiki/ ~~], [http://en.wikipedia.org/wiki/Callithrix_jacchus Callithrix jacchus~~] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p5j]] is a 81 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P5J FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6p4g\|6p4g]], [[6p4h\|6p4h]], [[6p5i\|6p5i]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6p4g\|6p4g]], [[6p4h\|6p4h]], [[6p5i\|6p5i]]</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6p5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5j OCA], [http://pdbe.org/6p5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p5j RCSB], [http://www.ebi.ac.uk/pdbsum/6p5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5j ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6p5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5j OCA], [http://pdbe.org/6p5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p5j RCSB], [http://www.ebi.ac.uk/pdbsum/6p5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5j ProSAT]</span></td></tr>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Callithrix jacchus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Oryctolagus cuniculus]]		[[Category: Oryctolagus cuniculus]]

OCA at 09:35, 8 January 2020

OCA — Wed, 08 Jan 2020 09:35:59 GMT

←Older revision		Revision as of 09:35, 8 January 2020
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6p5j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6p5j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:38, 30 October 2019

OCA — Wed, 30 Oct 2019 09:38:15 GMT

←Older revision		Revision as of 09:38, 30 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6p5j is ~~ON HOLD~~	+	==Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)==
		+	<StructureSection load='6p5j' size='340' side='right'caption='[[6p5j]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6p5j]] is a 81 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Callithrix_jacchus Callithrix jacchus] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P5J FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6p4g\|6p4g]], [[6p4h\|6p4h]], [[6p5i\|6p5i]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6p5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p5j OCA], [http://pdbe.org/6p5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p5j RCSB], [http://www.ebi.ac.uk/pdbsum/6p5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p5j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/U3KPD5_RABIT U3KPD5_RABIT]] Binds to the 23S rRNA.[RuleBase:RU000576] [[http://www.uniprot.org/uniprot/G1SS70_RABIT G1SS70_RABIT]] May play a role during erythropoiesis through regulation of transcription factor DDIT3.[HAMAP-Rule:MF_03122]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.

-	~~Authors~~:	+	The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.,Acosta-Reyes F, Neupane R, Frank J, Fernandez IS EMBO J. 2019 Oct 14:e102226. doi: 10.15252/embj.2019102226. PMID:31609474<ref>PMID:31609474</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6p5j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Callithrix jacchus]]
		+	[[Category: Large Structures]]
		+	[[Category: Oryctolagus cuniculus]]
		+	[[Category: Acosta-Reyes, F J]]
		+	[[Category: Fernandez, I S]]
		+	[[Category: Frank, J]]
		+	[[Category: Neupane, R]]
		+	[[Category: Internal ribosome entry site]]
		+	[[Category: Ire]]
		+	[[Category: Israeli acute paralysis virus]]
		+	[[Category: Large ribosomal subunit]]
		+	[[Category: Ribosome]]
		+	[[Category: Small ribosomal subunit]]

OCA: Protected "6p5j" [edit=sysop:move=sysop]

OCA — Wed, 12 Jun 2019 04:01:49 GMT

Protected "6p5j" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:01, 12 June 2019

OCA: New page: '''Unreleased structure''' The entry 6p5j is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 12 Jun 2019 04:01:48 GMT

New page: '''Unreleased structure''' The entry 6p5j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6p5j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]