4j0x - Revision history

OCA at 08:53, 20 March 2024

OCA — Wed, 20 Mar 2024 08:53:36 GMT

←Older revision		Revision as of 08:53, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4j0x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J0X FirstGlance]. <br>		<table><tr><td colspan='2'>[[4j0x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J0X 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=4j0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j0x OCA], [https://pdbe.org/4j0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j0x RCSB], [https://www.ebi.ac.uk/pdbsum/4j0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j0x ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.502Å</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=4j0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j0x OCA], [https://pdbe.org/4j0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j0x RCSB], [https://www.ebi.ac.uk/pdbsum/4j0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j0x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>		[https://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The U3 snoRNA is required for 18S rRNA processing and small subunit ribosome formation in eukaryotes. Different from other box C/D snoRNAs, U3 contains an extra 5' domain that pairs with pre-rRNA and a unique B/C motif essential for recruitment of the U3-specific Rrp9 protein. Here, we analyze the structure and function of Rrp9 with crystallographic, biochemical, and cellular approaches. Rrp9 is composed of a WD repeat domain and an N-terminal region. The crystal structures of the WD domain of yeast Rrp9 and its human ortholog U3-55K were determined, revealing a typical seven-bladed propeller fold. Several conserved surface patches on the WD domain were identified, and their function in RNP assembly and yeast growth were analyzed by mutagenesis. Prior association of Snu13 with the B/C motif was found to enhance the specific binding of the WD domain. We show that a conserved 7bc loop is crucial for specific recognition of U3, nucleolar localization of Rrp9, and yeast growth. In addition, we show that the N-terminal region of Rrp9 contains a bipartite nuclear localization signal that is dispensable for nucleolar localization. Our results provide insight into the functional sites of Rrp9.
-
-	Structural and functional analysis of the U3 snoRNA binding protein Rrp9.,Zhang L, Lin J, Ye K RNA. 2013 May;19(5):701-11. doi: 10.1261/rna.037580.112. Epub 2013 Mar 18. PMID:23509373<ref>PMID:23509373</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4j0x" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:22, 16 November 2022

OCA — Wed, 16 Nov 2022 21:22:41 GMT

←Older revision		Revision as of 21:22, 16 November 2022
Line 1:		Line 1:

	==Structure of Rrp9==		==Structure of Rrp9==
-	<StructureSection load='4j0x' size='340' side='right' caption='[[4j0x]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4j0x' size='340' side='right'caption='[[4j0x]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4j0x]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J0X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4J0X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4j0x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J0X FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RRP9, YPR137W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>	+	</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=4j0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j0x OCA], [https://pdbe.org/4j0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j0x RCSB], [https://www.ebi.ac.uk/pdbsum/4j0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j0x 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=4j0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j0x OCA], [~~http~~://pdbe.org/4j0x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4j0x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4j0x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4j0x ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>	+	[https://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lin, J~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Ye, K~~]]	+	[[Category: Lin J]]
-	[[Category: ~~Zhang, L~~]]	+	[[Category: Ye K]]
-	[[Category: ~~Beta-propeller]]~~	+	[[Category: Zhang L]]
-	~~[[Category: Preribosome]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Wd domain~~]]	+

OCA at 23:05, 5 August 2016

OCA — Fri, 05 Aug 2016 23:05:52 GMT

←Older revision		Revision as of 23:05, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of Rrp9==		==Structure of Rrp9==
	<StructureSection load='4j0x' size='340' side='right' caption='[[4j0x]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4j0x' size='340' side='right' caption='[[4j0x]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4j0x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J0X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J0X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4j0x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J0X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J0X FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RRP9, YPR137W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 ~~Saccharomyces cerevisiae S288c~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RRP9, YPR137W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4j0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j0x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j0x RCSB], [http://www.ebi.ac.uk/pdbsum/4j0x PDBsum]</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=4j0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j0x OCA], [http://pdbe.org/4j0x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j0x RCSB], [http://www.ebi.ac.uk/pdbsum/4j0x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j0x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4j0x" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae s288c~~]]	+	[[Category: Baker's yeast]]
	[[Category: Lin, J]]		[[Category: Lin, J]]
	[[Category: Ye, K]]		[[Category: Ye, K]]

OCA at 22:43, 25 December 2014

OCA — Thu, 25 Dec 2014 22:43:38 GMT

←Older revision		Revision as of 22:43, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4j0x\| PDB~~=4j0x \| ~~SCENE~~= }}	+	==Structure of Rrp9==
-	===~~Structure of Rrp9~~===	+	<StructureSection load='4j0x' size='340' side='right' caption='[[4j0x]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23509373}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4j0x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J0X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J0X FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RRP9, YPR137W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Saccharomyces cerevisiae S288c])</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=4j0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j0x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j0x RCSB], [http://www.ebi.ac.uk/pdbsum/4j0x PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>		[[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The U3 snoRNA is required for 18S rRNA processing and small subunit ribosome formation in eukaryotes. Different from other box C/D snoRNAs, U3 contains an extra 5' domain that pairs with pre-rRNA and a unique B/C motif essential for recruitment of the U3-specific Rrp9 protein. Here, we analyze the structure and function of Rrp9 with crystallographic, biochemical, and cellular approaches. Rrp9 is composed of a WD repeat domain and an N-terminal region. The crystal structures of the WD domain of yeast Rrp9 and its human ortholog U3-55K were determined, revealing a typical seven-bladed propeller fold. Several conserved surface patches on the WD domain were identified, and their function in RNP assembly and yeast growth were analyzed by mutagenesis. Prior association of Snu13 with the B/C motif was found to enhance the specific binding of the WD domain. We show that a conserved 7bc loop is crucial for specific recognition of U3, nucleolar localization of Rrp9, and yeast growth. In addition, we show that the N-terminal region of Rrp9 contains a bipartite nuclear localization signal that is dispensable for nucleolar localization. Our results provide insight into the functional sites of Rrp9.

-	~~==About this Structure==~~	+	Structural and functional analysis of the U3 snoRNA binding protein Rrp9.,Zhang L, Lin J, Ye K RNA. 2013 May;19(5):701-11. doi: 10.1261/rna.037580.112. Epub 2013 Mar 18. PMID:23509373<ref>PMID:23509373</ref>
-	~~[[4j0x]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4J0X OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023509373</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae s288c]]		[[Category: Saccharomyces cerevisiae s288c]]
-	[[Category: Lin, J.]]	+	[[Category: Lin, J]]
-	[[Category: Ye, K.]]	+	[[Category: Ye, K]]
-	[[Category: Zhang, L.]]	+	[[Category: Zhang, L]]
	[[Category: Beta-propeller]]		[[Category: Beta-propeller]]
	[[Category: Preribosome]]		[[Category: Preribosome]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]
	[[Category: Wd domain]]		[[Category: Wd domain]]

OCA at 15:54, 19 June 2013

OCA — Wed, 19 Jun 2013 15:54:43 GMT

←Older revision		Revision as of 15:54, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4j0x\| PDB=4j0x \| SCENE= }}
		+	===Structure of Rrp9===
		+	{{ABSTRACT_PUBMED_23509373}}

-	~~The entry 4j0x is ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/RRP9_YEAST RRP9_YEAST]] Involved in nucleolar processing of pre-18S ribosomal RNA. Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and biosynthesis of 18S rRNA.<ref>PMID:11105764</ref>

-	~~Authors~~: ~~Zhang, L~~.~~, Lin, J~~.~~, Ye, K~~.	+	==About this Structure==
		+	[[4j0x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J0X OCA].

-	~~Description~~: ~~Structure of Rrp9~~	+	==Reference==
		+	<ref group="xtra">PMID:023509373</ref><references group="xtra"/><references/>
		+	[[Category: Saccharomyces cerevisiae s288c]]
		+	[[Category: Lin, J.]]
		+	[[Category: Ye, K.]]
		+	[[Category: Zhang, L.]]
		+	[[Category: Beta-propeller]]
		+	[[Category: Preribosome]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Wd domain]]

OCA at 13:28, 20 February 2013

OCA — Wed, 20 Feb 2013 13:28:28 GMT

←Older revision		Revision as of 13:28, 20 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4j0x is ON HOLD	+	The entry 4j0x is ON HOLD until Paper Publication

	Authors: Zhang, L., Lin, J., Ye, K.		Authors: Zhang, L., Lin, J., Ye, K.

	Description: Structure of Rrp9		Description: Structure of Rrp9

OCA at 10:08, 13 February 2013

OCA — Wed, 13 Feb 2013 10:08:44 GMT

←Older revision		Revision as of 10:08, 13 February 2013
Line 3:		Line 3:
	The entry 4j0x is ON HOLD		The entry 4j0x is ON HOLD

-	Authors: ~~Liman~~ Zhang, ~~Jinzhong~~ Lin, ~~Keqiong~~ Ye	+	Authors: Zhang, L., Lin, J., Ye, K.

-	Description: Rrp9	+	Description: Structure of Rrp9

OCA: Protected "4j0x" [edit=sysop:move=sysop]

OCA — Wed, 06 Feb 2013 12:34:23 GMT

Protected "4j0x" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:34, 6 February 2013

OCA: New page: '''Unreleased structure''' The entry 4j0x is ON HOLD Authors: Liman Zhang, Jinzhong Lin, Keqiong Ye Description: Rrp9

OCA — Wed, 06 Feb 2013 12:34:22 GMT

New page: '''Unreleased structure''' The entry 4j0x is ON HOLD Authors: Liman Zhang, Jinzhong Lin, Keqiong Ye Description: Rrp9

New page

'''Unreleased structure'''

The entry 4j0x is ON HOLD

Authors: Liman Zhang, Jinzhong Lin, Keqiong Ye

Description: Rrp9