4jhj - Revision history

OCA at 15:42, 20 September 2023

OCA — Wed, 20 Sep 2023 15:42:33 GMT

←Older revision		Revision as of 15:42, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jhj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JHJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jhj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JHJ 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=4jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhj OCA], [https://pdbe.org/4jhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jhj RCSB], [https://www.ebi.ac.uk/pdbsum/4jhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jhj 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]] 3.25Å</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=4jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhj OCA], [https://pdbe.org/4jhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jhj RCSB], [https://www.ebi.ac.uk/pdbsum/4jhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jhj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 11:13, 24 November 2022

OCA — Thu, 24 Nov 2022 11:13:43 GMT

←Older revision		Revision as of 11:13, 24 November 2022
Line 1:		Line 1:

	==Crystal structure of Danio rerio Slip1 in complex with Dbp5==		==Crystal structure of Danio rerio Slip1 in complex with Dbp5==
-	<StructureSection load='4jhj' size='340' side='right' caption='[[4jhj]], [[Resolution\|resolution]] 3.25Å' scene=''>	+	<StructureSection load='4jhj' size='340' side='right'caption='[[4jhj]], [[Resolution\|resolution]] 3.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jhj]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JHJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jhj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JHJ FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fht\|3fht]], [[3fhc\|3fhc]], [[2i2o\|2i2o]], [[4jhk\|4jhk]]</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=4jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhj OCA], [https://pdbe.org/4jhj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jhj RCSB], [https://www.ebi.ac.uk/pdbsum/4jhj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jhj ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mif4gdb, zgc:110826 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), ddx19 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=4jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhj OCA], [~~http~~://pdbe.org/4jhj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jhj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jhj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jhj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/M4GDB_DANRE M4GDB_DANRE]] Functions in replication-dependent translation of histone mRNAs which differ from other eukaryotic mRNAs in that they do not end with a poly-A tail but a stem-loop. May participate in circularizing those mRNAs specifically enhancing their translation (By similarity).	+	[https://www.uniprot.org/uniprot/M4GDB_DANRE M4GDB_DANRE] Functions in replication-dependent translation of histone mRNAs which differ from other eukaryotic mRNAs in that they do not end with a poly-A tail but a stem-loop. May participate in circularizing those mRNAs specifically enhancing their translation (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
-	[[Category: ~~Conti, E~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Moeller, H Von~~]]	+	[[Category: Conti E]]
-	[[Category: ~~3'-processing]]~~	+	[[Category: Von Moeller H]]
-	~~[[Category: 3'-utr]]~~	+
-	~~[[Category: Atp binding]]~~	+
-	~~[[Category: Ddx19]]~~	+
-	~~[[Category: Dead-box helicase]]~~	+
-	~~[[Category: Dead-box protein 19b]]~~	+
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mrna export]]~~	+
-	~~[[Category: Mrna transport]]~~	+
-	~~[[Category: Nucleotide binding]]~~	+
-	~~[[Category: Nup214]]~~	+
-	~~[[Category: Reca-like]]~~	+
-	~~[[Category: Rna binding]]~~	+
-	~~[[Category: Rna-dependent atpase]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Transport histone mrna processing~~]]	+

OCA at 16:20, 11 August 2016

OCA — Thu, 11 Aug 2016 16:20:25 GMT

←Older revision		Revision as of 16:20, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Danio rerio Slip1 in complex with Dbp5==		==Crystal structure of Danio rerio Slip1 in complex with Dbp5==
	<StructureSection load='4jhj' size='340' side='right' caption='[[4jhj]], [[Resolution\|resolution]] 3.25Å' scene=''>		<StructureSection load='4jhj' size='340' side='right' caption='[[4jhj]], [[Resolution\|resolution]] 3.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jhj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Danio_rerio Danio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JHJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jhj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JHJ FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fht\|3fht]], [[3fhc\|3fhc]], [[2i2o\|2i2o]], [[4jhk\|4jhk]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fht\|3fht]], [[3fhc\|3fhc]], [[2i2o\|2i2o]], [[4jhk\|4jhk]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mif4gdb, zgc:110826 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 ~~Danio~~ rerio]), ddx19 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 ~~Danio~~ rerio])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mif4gdb, zgc:110826 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), ddx19 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=4jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jhj RCSB], [http://www.ebi.ac.uk/pdbsum/4jhj 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=4jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhj OCA], [http://pdbe.org/4jhj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jhj RCSB], [http://www.ebi.ac.uk/pdbsum/4jhj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jhj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/M4GDB_DANRE M4GDB_DANRE]] Functions in replication-dependent translation of histone mRNAs which differ from other eukaryotic mRNAs in that they do not end with a poly-A tail but a stem-loop. May participate in circularizing those mRNAs specifically enhancing their translation (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 18:
	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 4jhj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Danio~~ rerio]]	+	[[Category: Brachidanio rerio]]
	[[Category: Conti, E]]		[[Category: Conti, E]]
	[[Category: Moeller, H Von]]		[[Category: Moeller, H Von]]

OCA at 10:29, 25 January 2015

OCA — Sun, 25 Jan 2015 10:29:44 GMT

←Older revision		Revision as of 10:29, 25 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4jhj\| PDB=4jhj \| SCENE= }}~~	+	==Crystal structure of Danio rerio Slip1 in complex with Dbp5==
-	===Crystal structure of Danio rerio Slip1 in complex with Dbp5===	+	<StructureSection load='4jhj' size='340' side='right' caption='[[4jhj]], [[Resolution\|resolution]] 3.25Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23804756}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4jhj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JHJ FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fht\|3fht]], [[3fhc\|3fhc]], [[2i2o\|2i2o]], [[4jhk\|4jhk]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mif4gdb, zgc:110826 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Danio rerio]), ddx19 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Danio rerio])</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=4jhj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jhj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jhj RCSB], [http://www.ebi.ac.uk/pdbsum/4jhj PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In metazoans, replication-dependent histone mRNAs end in a stem-loop structure instead of the poly(A) tail characteristic of all other mature mRNAs. This specialized 3' end is bound by stem-loop binding protein (SLBP), a protein that participates in the nuclear export and translation of histone mRNAs. The translational activity of SLBP is mediated by interaction with SLIP1, a middle domain of initiation factor 4G (MIF4G)-like protein that connects to translation initiation. We determined the 2.5 A resolution crystal structure of zebrafish SLIP1 bound to the translation-activation domain of SLBP and identified the determinants of the recognition. We discovered a SLIP1-binding motif (SBM) in two additional proteins: the translation initiation factor eIF3g and the mRNA-export factor DBP5. We confirmed the binding of SLIP1 to DBP5 and eIF3g by pull-down assays and determined the 3.25 A resolution structure of SLIP1 bound to the DBP5 SBM. The SBM-binding and homodimerization residues of SLIP1 are conserved in the MIF4G domain of CBP80/20-dependent translation initiation factor (CTIF). The results suggest how the SLIP1 homodimer or a SLIP1-CTIF heterodimer can function as platforms to bridge SLBP with SBM-containing proteins involved in different steps of mRNA metabolism.

-	~~==About this Structure==~~	+	Structural and biochemical studies of SLIP1-SLBP identify DBP5 and eIF3g as SLIP1-binding proteins.,von Moeller H, Lerner R, Ricciardi A, Basquin C, Marzluff WF, Conti E Nucleic Acids Res. 2013 Jun 26. PMID:23804756<ref>PMID:23804756</ref>
-	~~[[4jhj]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Danio_rerio Danio rerio]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023804756</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Danio rerio]]		[[Category: Danio rerio]]
-	[[Category: Conti, E.]]	+	[[Category: Conti, E]]
-	[[Category: Moeller, H Von.]]	+	[[Category: Moeller, H Von]]
	[[Category: 3'-processing]]		[[Category: 3'-processing]]
	[[Category: 3'-utr]]		[[Category: 3'-utr]]

OCA at 15:37, 10 July 2013

OCA — Wed, 10 Jul 2013 15:37:10 GMT

←Older revision		Revision as of 15:37, 10 July 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4jhj\| PDB=4jhj \| SCENE= }}
		+	===Crystal structure of Danio rerio Slip1 in complex with Dbp5===
		+	{{ABSTRACT_PUBMED_23804756}}

-	~~The entry~~ 4jhj is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4jhj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JHJ OCA].

-	~~Authors~~: ~~Von Moeller, H.,~~ Conti, E.	+	==Reference==
-		+	<ref group="xtra">PMID:023804756</ref><references group="xtra"/><references/>
-	~~Description~~:	+	[[Category: Danio rerio]]
		+	[[Category: Conti, E.]]
		+	[[Category: Moeller, H Von.]]
		+	[[Category: 3'-processing]]
		+	[[Category: 3'-utr]]
		+	[[Category: Atp binding]]
		+	[[Category: Ddx19]]
		+	[[Category: Dead-box helicase]]
		+	[[Category: Dead-box protein 19b]]
		+	[[Category: Helicase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mrna export]]
		+	[[Category: Mrna transport]]
		+	[[Category: Nucleotide binding]]
		+	[[Category: Nup214]]
		+	[[Category: Reca-like]]
		+	[[Category: Rna binding]]
		+	[[Category: Rna-dependent atpase]]
		+	[[Category: Translation]]
		+	[[Category: Transport histone mrna processing]]

OCA at 19:54, 17 April 2013

OCA — Wed, 17 Apr 2013 19:54:14 GMT

←Older revision		Revision as of 19:54, 17 April 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Von Moeller, H., Conti, E.		Authors: Von Moeller, H., Conti, E.

	Description:		Description:

OCA at 16:19, 20 March 2013

OCA — Wed, 20 Mar 2013 16:19:31 GMT

←Older revision		Revision as of 16:19, 20 March 2013
Line 5:		Line 5:
	Authors: Von Moeller, H., Conti, E.		Authors: Von Moeller, H., Conti, E.

-	Description: ~~xray structure of a protein complex, title to be announced~~	+	Description:

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

OCA — Wed, 13 Mar 2013 10:01:37 GMT

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

←Older revision

Revision as of 10:01, 13 March 2013

OCA: New page: '''Unreleased structure''' The entry 4jhj is ON HOLD Authors: Von Moeller, H., Conti, E. Description: xray structure of a protein complex, title to be announced

OCA — Wed, 13 Mar 2013 10:01:36 GMT

New page: '''Unreleased structure''' The entry 4jhj is ON HOLD Authors: Von Moeller, H., Conti, E. Description: xray structure of a protein complex, title to be announced

New page

'''Unreleased structure'''

The entry 4jhj is ON HOLD

Authors: Von Moeller, H., Conti, E.

Description: xray structure of a protein complex, title to be announced