6n3e - Revision history

OCA at 14:46, 13 March 2024

OCA — Wed, 13 Mar 2024 14:46:15 GMT

←Older revision		Revision as of 14:46, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6n3e' size='340' side='right'caption='[[6n3e]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='6n3e' size='340' side='right'caption='[[6n3e]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n3e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N3E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N3E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n3e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N3E FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FMT:FORMIC+ACID'>FMT</scene~~>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~</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]] 1.893Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HTATSF1 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=6n3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n3e OCA], [~~http~~://pdbe.org/6n3e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n3e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n3e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n3e 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=6n3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n3e OCA], [https://pdbe.org/6n3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n3e RCSB], [https://www.ebi.ac.uk/pdbsum/6n3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n3e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HTSF1_HUMAN HTSF1_HUMAN]] Functions as a general transcription factor playing a role in the process of transcriptional elongation. May mediate the reciprocal stimulatory effect of splicing on transcriptional elongation. In case of infection by HIV-1, it is up-regulated by the HIV-1 proteins NEF and gp120, acts as a cofactor required for the Tat-enhanced transcription of the virus.<ref>PMID:10393184</ref> <ref>PMID:10454543</ref> <ref>PMID:10913173</ref> <ref>PMID:11420046</ref> <ref>PMID:11780068</ref> <ref>PMID:15905670</ref> <ref>PMID:8849451</ref> <ref>PMID:9765201</ref>	+	[https://www.uniprot.org/uniprot/HTSF1_HUMAN HTSF1_HUMAN] Functions as a general transcription factor playing a role in the process of transcriptional elongation. May mediate the reciprocal stimulatory effect of splicing on transcriptional elongation. In case of infection by HIV-1, it is up-regulated by the HIV-1 proteins NEF and gp120, acts as a cofactor required for the Tat-enhanced transcription of the virus.<ref>PMID:10393184</ref> <ref>PMID:10454543</ref> <ref>PMID:10913173</ref> <ref>PMID:11420046</ref> <ref>PMID:11780068</ref> <ref>PMID:15905670</ref> <ref>PMID:8849451</ref> <ref>PMID:9765201</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The transcription elongation and pre-mRNA splicing factor Tat-SF1 associates with the U2 small nuclear ribonucleoprotein (snRNP) of the spliceosome. However, the direct binding partner and underlying interactions mediating the Tat-SF1-U2 snRNP association remain unknown. Here, we identified SF3b1 as a Tat-SF1-interacting subunit of the U2 snRNP. Our 1.1 A resolution crystal structure revealed that Tat-SF1 contains a U2AF homology motif (UHM) protein-protein interaction module. We demonstrated that Tat-SF1 preferentially and directly binds the SF3b1 subunit compared to other U2AF ligand motif (ULM)-containing splicing factors, and further established that SF3b1 association depends on the integrity of the Tat-SF1 UHM. We next compared the Tat-SF1 binding affinities for each of the five known SF3b1 ULMs and then determined the structures of representative high- and low-affinity SF3b1 ULM complexes with the Tat-SF1 UHM at 1.9 A and 2.1 A resolutions, respectively. These structures revealed a canonical UHM-ULM interface, comprising a Tat-SF1 binding pocket for a ULM tryptophan (SF3b1 W338) and electrostatic interactions with a basic ULM tail. Importantly, we found that SF3b1 regulates Tat-SF1 levels and that these two factors influence expression of overlapping representative transcripts, consistent with a functional partnership of Tat-SF1 and SF3b1. Altogether, these results define a new molecular interface of the Tat-SF1-U2 snRNP complex for gene regulation.	+
-		+
-	The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface.,Loerch S, Leach JR, Horner SW, Maji D, Jenkins JL, Pulvino M, Kielkopf CL J Biol Chem. 2018 Dec 19. pii: RA118.006764. doi: 10.1074/jbc.RA118.006764. PMID:30567737<ref>PMID:30567737</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6n3e" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jenkins~~, J L~~]]	+	[[Category: Jenkins JL]]
-	[[Category: Kielkopf~~, C L~~]]	+	[[Category: Kielkopf CL]]
-	[[Category: Loerch, S]]	+	[[Category: Loerch S]]
-	~~[[Category: Hiv tat-specific factor 1]]~~	+
-	~~[[Category: Pre-mrna splicing factor]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Protein-peptide complex]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna splicing factor]]~~	+
-	~~[[Category: U2af homology motif]]~~	+
-	~~[[Category: U2af ligand motif]]~~	+
-	~~[[Category: Uhm]]~~	+
-	~~[[Category: Ulm~~]]	+

OCA at 11:17, 18 December 2019

OCA — Wed, 18 Dec 2019 11:17:23 GMT

←Older revision		Revision as of 11:17, 18 December 2019
Line 1:		Line 1:

	==Structure of HIV Tat-specific factor 1 U2AF Homology Motif bound to U2AF ligand motif 4==		==Structure of HIV Tat-specific factor 1 U2AF Homology Motif bound to U2AF ligand motif 4==
-	<StructureSection load='6n3e' size='340' side='right' caption='[[6n3e]], [[Resolution\|resolution]] 1.89Å' scene=''>	+	<StructureSection load='6n3e' size='340' side='right'caption='[[6n3e]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6n3e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N3E FirstGlance]. <br>		<table><tr><td colspan='2'>[[6n3e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N3E FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Jenkins, J L]]		[[Category: Jenkins, J L]]
	[[Category: Kielkopf, C L]]		[[Category: Kielkopf, C L]]

OCA at 08:31, 6 March 2019

OCA — Wed, 06 Mar 2019 08:31:21 GMT

←Older revision		Revision as of 08:31, 6 March 2019
Line 1:		Line 1:

	==Structure of HIV Tat-specific factor 1 U2AF Homology Motif bound to U2AF ligand motif 4==		==Structure of HIV Tat-specific factor 1 U2AF Homology Motif bound to U2AF ligand motif 4==
-	<StructureSection load='6n3e' size='340' side='right' caption='[[6n3e]], [[Resolution\|resolution]] 1.89Å' scene=''>	+	<StructureSection load='6n3e' size='340' side='right' caption='[[6n3e]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n3e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N3E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n3e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N3E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HTATSF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6n3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n3e OCA], [http://pdbe.org/6n3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n3e RCSB], [http://www.ebi.ac.uk/pdbsum/6n3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n3e 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=6n3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n3e OCA], [http://pdbe.org/6n3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n3e RCSB], [http://www.ebi.ac.uk/pdbsum/6n3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n3e ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Jenkins, J L]]		[[Category: Jenkins, J L]]
	[[Category: Kielkopf, C L]]		[[Category: Kielkopf, C L]]

OCA at 06:13, 2 January 2019

OCA — Wed, 02 Jan 2019 06:13:13 GMT

←Older revision		Revision as of 06:13, 2 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n3e is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of HIV Tat-specific factor 1 U2AF Homology Motif bound to U2AF ligand motif 4==
		+	<StructureSection load='6n3e' size='340' side='right' caption='[[6n3e]], [[Resolution\|resolution]] 1.89Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n3e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N3E FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=6n3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n3e OCA], [http://pdbe.org/6n3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n3e RCSB], [http://www.ebi.ac.uk/pdbsum/6n3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n3e ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HTSF1_HUMAN HTSF1_HUMAN]] Functions as a general transcription factor playing a role in the process of transcriptional elongation. May mediate the reciprocal stimulatory effect of splicing on transcriptional elongation. In case of infection by HIV-1, it is up-regulated by the HIV-1 proteins NEF and gp120, acts as a cofactor required for the Tat-enhanced transcription of the virus.<ref>PMID:10393184</ref> <ref>PMID:10454543</ref> <ref>PMID:10913173</ref> <ref>PMID:11420046</ref> <ref>PMID:11780068</ref> <ref>PMID:15905670</ref> <ref>PMID:8849451</ref> <ref>PMID:9765201</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The transcription elongation and pre-mRNA splicing factor Tat-SF1 associates with the U2 small nuclear ribonucleoprotein (snRNP) of the spliceosome. However, the direct binding partner and underlying interactions mediating the Tat-SF1-U2 snRNP association remain unknown. Here, we identified SF3b1 as a Tat-SF1-interacting subunit of the U2 snRNP. Our 1.1 A resolution crystal structure revealed that Tat-SF1 contains a U2AF homology motif (UHM) protein-protein interaction module. We demonstrated that Tat-SF1 preferentially and directly binds the SF3b1 subunit compared to other U2AF ligand motif (ULM)-containing splicing factors, and further established that SF3b1 association depends on the integrity of the Tat-SF1 UHM. We next compared the Tat-SF1 binding affinities for each of the five known SF3b1 ULMs and then determined the structures of representative high- and low-affinity SF3b1 ULM complexes with the Tat-SF1 UHM at 1.9 A and 2.1 A resolutions, respectively. These structures revealed a canonical UHM-ULM interface, comprising a Tat-SF1 binding pocket for a ULM tryptophan (SF3b1 W338) and electrostatic interactions with a basic ULM tail. Importantly, we found that SF3b1 regulates Tat-SF1 levels and that these two factors influence expression of overlapping representative transcripts, consistent with a functional partnership of Tat-SF1 and SF3b1. Altogether, these results define a new molecular interface of the Tat-SF1-U2 snRNP complex for gene regulation.

-	~~Authors~~:	+	The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface.,Loerch S, Leach JR, Horner SW, Maji D, Jenkins JL, Pulvino M, Kielkopf CL J Biol Chem. 2018 Dec 19. pii: RA118.006764. doi: 10.1074/jbc.RA118.006764. PMID:30567737<ref>PMID:30567737</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6n3e" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Jenkins, J L]]
		+	[[Category: Kielkopf, C L]]
		+	[[Category: Loerch, S]]
		+	[[Category: Hiv tat-specific factor 1]]
		+	[[Category: Pre-mrna splicing factor]]
		+	[[Category: Protein binding]]
		+	[[Category: Protein-peptide complex]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rna splicing factor]]
		+	[[Category: U2af homology motif]]
		+	[[Category: U2af ligand motif]]
		+	[[Category: Uhm]]
		+	[[Category: Ulm]]

OCA at 05:19, 12 December 2018

OCA — Wed, 12 Dec 2018 05:19:07 GMT

←Older revision		Revision as of 05:19, 12 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n3e is ON HOLD	+	The entry 6n3e is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6n3e" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 19:12:00 GMT

Protected "6n3e" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:12, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n3e is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Sun, 02 Dec 2018 19:11:59 GMT

New page: '''Unreleased structure''' The entry 6n3e is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6n3e is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]