2y9c - Revision history

OCA: Redirecting to 4wzj

OCA — Thu, 06 Apr 2017 14:20:10 GMT

Redirecting to 4wzj

←Older revision		Revision as of 14:20, 6 April 2017
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-	#REDIRECT [[~~4v5u~~]] This PDB entry is obsolete and replaced by ~~4v5u~~	+	#REDIRECT [[4wzj]] This PDB entry is obsolete and replaced by 4wzj

OCA: Redirecting to 4v5u

OCA — Wed, 10 Dec 2014 15:18:32 GMT

Redirecting to 4v5u

←Older revision		Revision as of 15:18, 10 December 2014
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-	~~==STRUCTURE OF THE SPLICEOSOMAL U4 SNRNP CORE DOMAIN==~~	+	#REDIRECT [[4v5u]] This PDB entry is obsolete and replaced by 4v5u
-	~~<StructureSection load='2y9c' size='340' side='right' caption='~~[[~~2y9c]], [[Resolution\|resolution]] 3.60Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[2y9c~~]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y9C FirstGlance]. <br>	+
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2y9a\|2y9a]], [[2y9b\|2y9b]], [[2y9d\|2y9d]], [[1d3b\|1d3b]], [[1b34\|1b34]], [[3cw1\|3cw1]], [[3pgw\|3pgw]]</td></tr>	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RNU4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2y9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y9c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y9c RCSB], [http://www.ebi.ac.uk/pdbsum/2y9c PDBsum]</span></td></tr>	+
-	~~</table>~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~The spliceosome is a dynamic macromolecular machine that assembles on pre-messenger RNA substrates~~ and catalyses the excision of non-coding intervening sequences (introns). Four of the five major components of the spliceosome, U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), contain seven Sm proteins (SmB/B', SmD1, SmD2, SmD3, SmE, SmF and SmG) in common. Following export of the U1, U2, U4 and U5 snRNAs to the cytoplasm, the seven Sm proteins, chaperoned by the survival of motor neurons (SMN) complex, assemble around a single-stranded, U-rich sequence called the Sm site in each small nuclear RNA (snRNA), to form the core domain of the respective snRNP particle. Core domain formation is a prerequisite for re-import into the nucleus, where these snRNPs mature via addition of their particle-specific proteins. Here we present a crystal structure of the U4 snRNP core domain at 3.6 A resolution, detailing how the Sm site heptad (AUUUUUG) binds inside the central hole of the heptameric ring of Sm proteins, interacting one-to-one with SmE-SmG-SmD3-SmB-SmD1-SmD2-SmF. An irregular backbone conformation of the Sm site sequence combined with the asymmetric structure of the heteromeric protein ring allows each base to interact in a distinct manner with four key residues at equivalent positions in the L3 and L5 loops of the Sm fold. A comparison of this structure with the U1 snRNP at 5.5 A resolution reveals snRNA-dependent structural changes outside the Sm fold, which may facilitate the binding of particle-specific proteins that are crucial to biogenesis of spliceosomal snRNPs.	+
-		+
-	~~Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis.,Leung AK, Nagai K, Li J Nature. 2011 Apr 24. PMID:21516107<ref>PMID:21516107</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Homo sapiens]]~~	+
-	~~[[Category: Leung, A K.W.]]~~	+
-	~~[[Category: Li, J.]]~~	+
-	~~[[Category: Nagai, K.]]~~	+
-	~~[[Category: Heteromeric heptameric ring]]~~	+
-	~~[[Category: Pre-mrna splicing]]~~	+
-	~~[[Category: Rna binding]]~~	+
-	~~[[Category: Sm fold]]~~	+
-	~~[[Category: Sm site]]~~	+
-	~~[[Category: Snrnp biogenesis]]~~	+
-	~~[[Category: Spliceosome]]~~	+
-	~~[[Category: Splicing-rna complex]]~~	+

OCA at 11:56, 29 October 2014

OCA — Wed, 29 Oct 2014 11:56:21 GMT

←Older revision		Revision as of 11:56, 29 October 2014
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-	[[~~Image:~~2y9c.~~png~~\|~~left~~\|~~200px~~]]	+	==STRUCTURE OF THE SPLICEOSOMAL U4 SNRNP CORE DOMAIN==
		+	<StructureSection load='2y9c' size='340' side='right' caption='[[2y9c]], [[Resolution\|resolution]] 3.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2y9c]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y9C FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2y9a\|2y9a]], [[2y9b\|2y9b]], [[2y9d\|2y9d]], [[1d3b\|1d3b]], [[1b34\|1b34]], [[3cw1\|3cw1]], [[3pgw\|3pgw]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), SNRPG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RNU4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2y9c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y9c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2y9c RCSB], [http://www.ebi.ac.uk/pdbsum/2y9c PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The spliceosome is a dynamic macromolecular machine that assembles on pre-messenger RNA substrates and catalyses the excision of non-coding intervening sequences (introns). Four of the five major components of the spliceosome, U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), contain seven Sm proteins (SmB/B', SmD1, SmD2, SmD3, SmE, SmF and SmG) in common. Following export of the U1, U2, U4 and U5 snRNAs to the cytoplasm, the seven Sm proteins, chaperoned by the survival of motor neurons (SMN) complex, assemble around a single-stranded, U-rich sequence called the Sm site in each small nuclear RNA (snRNA), to form the core domain of the respective snRNP particle. Core domain formation is a prerequisite for re-import into the nucleus, where these snRNPs mature via addition of their particle-specific proteins. Here we present a crystal structure of the U4 snRNP core domain at 3.6 A resolution, detailing how the Sm site heptad (AUUUUUG) binds inside the central hole of the heptameric ring of Sm proteins, interacting one-to-one with SmE-SmG-SmD3-SmB-SmD1-SmD2-SmF. An irregular backbone conformation of the Sm site sequence combined with the asymmetric structure of the heteromeric protein ring allows each base to interact in a distinct manner with four key residues at equivalent positions in the L3 and L5 loops of the Sm fold. A comparison of this structure with the U1 snRNP at 5.5 A resolution reveals snRNA-dependent structural changes outside the Sm fold, which may facilitate the binding of particle-specific proteins that are crucial to biogenesis of spliceosomal snRNPs.

-	~~{{STRUCTURE_2y9c\| PDB=2y9c \| SCENE= }}~~	+	Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis.,Leung AK, Nagai K, Li J Nature. 2011 Apr 24. PMID:21516107<ref>PMID:21516107</ref>

-	~~===STRUCTURE OF THE SPLICEOSOMAL U4 SNRNP CORE DOMAIN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21516107}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2y9c]] is~~ a ~~24 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9C OCA].~~	+	</StructureSection>
-		+
-	~~==See Also==~~	+
-	*[[Nucleoprotein\|Nucleoprotein]]	+
-		+
-	~~==Reference==~~	+
-	<~~ref group="xtra"~~>~~PMID:021516107~~</~~ref~~>~~<ref group~~=~~"xtra">PMID:010025403</ref><ref group~~=~~"xtra">PMID:011331594</ref><ref group~~=~~"xtra">PMID:019325628</ref><ref group~~=~~"xtra">PMID:021113136~~</~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Leung, A K.W.]]		[[Category: Leung, A K.W.]]

OCA at 14:02, 20 October 2012

OCA — Sat, 20 Oct 2012 14:02:46 GMT

←Older revision		Revision as of 14:02, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[2y9c]] is a 24 chain structure ~~of [[Nucleoprotein]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9C OCA].	+	[[2y9c]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9C OCA].

	==See Also==		==See Also==

OCA at 13:52, 26 July 2012

OCA — Thu, 26 Jul 2012 13:52:25 GMT

←Older revision		Revision as of 13:52, 26 July 2012
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	[[Image:2y9c.png\|left\|200px]]		[[Image:2y9c.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2y9c", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2y9c\| PDB=2y9c \| SCENE= }}		{{STRUCTURE_2y9c\| PDB=2y9c \| SCENE= }}

	===STRUCTURE OF THE SPLICEOSOMAL U4 SNRNP CORE DOMAIN===		===STRUCTURE OF THE SPLICEOSOMAL U4 SNRNP CORE DOMAIN===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21516107}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21516107 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21516107}}		{{ABSTRACT_PUBMED_21516107}}

	==About this Structure==		==About this Structure==
-	[[2y9c]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9C OCA].	+	[[2y9c]] is a 24 chain structure of [[Nucleoprotein]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9C OCA].
		+
		+	==See Also==
		+	*[[Nucleoprotein\|Nucleoprotein]]

	==Reference==		==Reference==

OCA at 05:45, 20 July 2011

OCA — Wed, 20 Jul 2011 05:45:30 GMT

←Older revision		Revision as of 05:45, 20 July 2011
Line 27:		Line 27:
	[[Category: Li, J.]]		[[Category: Li, J.]]
	[[Category: Nagai, K.]]		[[Category: Nagai, K.]]
		+	[[Category: Heteromeric heptameric ring]]
		+	[[Category: Pre-mrna splicing]]
		+	[[Category: Rna binding]]
		+	[[Category: Sm fold]]
		+	[[Category: Sm site]]
		+	[[Category: Snrnp biogenesis]]
		+	[[Category: Spliceosome]]
		+	[[Category: Splicing-rna complex]]

OCA at 04:54, 1 June 2011

OCA — Wed, 01 Jun 2011 04:54:36 GMT

←Older revision		Revision as of 04:54, 1 June 2011
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-	[[Image:2y9c.~~jpg~~\|left\|200px]]	+	[[Image:2y9c.png\|left\|200px]]

	<!--		<!--

OCA at 04:44, 12 May 2011

OCA — Thu, 12 May 2011 04:44:47 GMT

←Older revision		Revision as of 04:44, 12 May 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:2y9c.jpg\|left\|200px]]

-	The ~~entry 2y9c~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2y9c", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_2y9c\| PDB=2y9c \| SCENE= }}

-	~~Authors: Leung, A.K.W., Nagai, K., Li, J.~~	+	===STRUCTURE OF THE SPLICEOSOMAL U4 SNRNP CORE DOMAIN===

-	~~Description~~: ~~Structure of~~ the ~~spliceosomal U4 snRNP core domain~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21516107}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21516107 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21516107}}
		+
		+	==About this Structure==
		+	[[2y9c]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9C OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021516107</ref><ref group="xtra">PMID:010025403</ref><ref group="xtra">PMID:011331594</ref><ref group="xtra">PMID:019325628</ref><ref group="xtra">PMID:021113136</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Leung, A K.W.]]
		+	[[Category: Li, J.]]
		+	[[Category: Nagai, K.]]

OCA at 06:28, 2 March 2011

OCA — Wed, 02 Mar 2011 06:28:57 GMT

←Older revision		Revision as of 06:28, 2 March 2011
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 2y9c is ON HOLD ~~until sometime in the future~~	+	The entry 2y9c is ON HOLD

	Authors: Leung, A.K.W., Nagai, K., Li, J.		Authors: Leung, A.K.W., Nagai, K., Li, J.

	Description: Structure of the spliceosomal U4 snRNP core domain		Description: Structure of the spliceosomal U4 snRNP core domain

OCA: Protected "2y9c" [edit=sysop:move=sysop]

OCA — Wed, 23 Feb 2011 09:29:58 GMT

Protected "2y9c" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:29, 23 February 2011