4o42 - Revision history

OCA at 17:06, 20 September 2023

OCA — Wed, 20 Sep 2023 17:06:54 GMT

←Older revision		Revision as of 17:06, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o42]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Hong_Kong/5/1983(H3N2)) Influenza A virus (A/Hong Kong/5/1983(H3N2))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O42 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o42]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Hong_Kong/5/1983(H3N2)) Influenza A virus (A/Hong Kong/5/1983(H3N2))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O42 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 1.87Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></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=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [https://pdbe.org/4o42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [https://www.ebi.ac.uk/pdbsum/4o42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o42 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=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [https://pdbe.org/4o42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [https://www.ebi.ac.uk/pdbsum/4o42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o42 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	==See Also==		==See Also==
	*[[Chromodomain-helicase-DNA-binding protein 3D structures\|Chromodomain-helicase-DNA-binding protein 3D structures]]		*[[Chromodomain-helicase-DNA-binding protein 3D structures\|Chromodomain-helicase-DNA-binding protein 3D structures]]
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:55, 18 January 2023

OCA — Wed, 18 Jan 2023 08:55:10 GMT

←Older revision		Revision as of 08:55, 18 January 2023
Line 1:		Line 1:

	==Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229==		==Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229==
-	<StructureSection load='4o42' size='340' side='right' caption='[[4o42]], [[Resolution\|resolution]] 1.87Å' scene=''>	+	<StructureSection load='4o42' size='340' side='right'caption='[[4o42]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4o42]] 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=4O42 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4O42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4o42]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Hong_Kong/5/1983(H3N2)) Influenza A virus (A/Hong Kong/5/1983(H3N2))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O42 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, ~~<scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene><~~/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=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [https://pdbe.org/4o42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [https://www.ebi.ac.uk/pdbsum/4o42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o42 ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [~~http~~://pdbe.org/4o42 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4o42 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4o42 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</ref> [[http://www.uniprot.org/uniprot/NS1_I83A8 NS1_I83A8]] Inhibits post-transcriptional processing of cellular pre-mRNA, by binding and inhibiting two cellular proteins that are required for the 3'-end processing of cellular pre-mRNAs: the 30 kDa cleavage and polyadenylation specificity factor (CPSF4) and the poly(A)-binding protein 2 (PABPN1). This results in the accumulation of unprocessed 3' end pre-mRNAs which can't be exported from the nucleus. Cellular protein synthesis is thereby shut off very early after virus infection. Viral protein synthesis is not affected by the inhibition of the cellular 3' end processing machinery because the poly(A) tails of viral mRNAs are produced by the viral polymerase through a stuttering mechanism (By similarity). Prevents the establishment of the cellular antiviral state by inhibiting TRIM25-mediated DDX58 ubiquitination, which normally triggers the antiviral transduction signal that leads to the activation of type I IFN genes by transcription factors like IRF3 and IRF7. Prevents human EIF2AK2/PKR activation, either by binding double-strand RNA, or by interacting directly with EIF2AK2/PKR. This function may be important at the very beginning of the infection, when NS1 is mainly present in the cytoplasm. Also binds poly(A) and U6 snRNA. Suppresses the RNA silencing-based antiviral response in Drosophila cells (By similarity).	+	[https://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4o42" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4o42" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Chromodomain-helicase-DNA-binding protein 3D structures\|Chromodomain-helicase-DNA-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA helicase~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Bountra, C]]	+	[[Category: Bountra C]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Edwards AM]]
-	[[Category: Min, J]]	+	[[Category: Min J]]
-	[[Category: Qin, S]]	+	[[Category: Qin S]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Tempel W]]
-	[[Category: Tempel, W]]	+	[[Category: Xu C]]
-	[[Category: Xu, C]]	+
-	~~[[Category: Chromodomain]]~~	+
-	~~[[Category: Dna binding protein-viral protein complex]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Viral~~]]	+

OCA at 07:57, 4 August 2016

OCA — Thu, 04 Aug 2016 07:57:44 GMT

←Older revision		Revision as of 07:57, 4 August 2016
Line 1:		Line 1:
		+
	==Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229==		==Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229==
	<StructureSection load='4o42' size='340' side='right' caption='[[4o42]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='4o42' size='340' side='right' caption='[[4o42]], [[Resolution\|resolution]] 1.87Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [http://www.ebi.ac.uk/pdbsum/4o42 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=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [http://pdbe.org/4o42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [http://www.ebi.ac.uk/pdbsum/4o42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o42 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4o42" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:07, 25 December 2014

OCA — Thu, 25 Dec 2014 07:07:56 GMT

←Older revision		Revision as of 07:07, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o42]] 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=4O42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O42 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o42]] 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=4O42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O42 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [http://www.ebi.ac.uk/pdbsum/4o42 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=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [http://www.ebi.ac.uk/pdbsum/4o42 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</ref> [[http://www.uniprot.org/uniprot/NS1_I83A8 NS1_I83A8]] Inhibits post-transcriptional processing of cellular pre-mRNA, by binding and inhibiting two cellular proteins that are required for the 3'-end processing of cellular pre-mRNAs: the 30 kDa cleavage and polyadenylation specificity factor (CPSF4) and the poly(A)-binding protein 2 (PABPN1). This results in the accumulation of unprocessed 3' end pre-mRNAs which can't be exported from the nucleus. Cellular protein synthesis is thereby shut off very early after virus infection. Viral protein synthesis is not affected by the inhibition of the cellular 3' end processing machinery because the poly(A) tails of viral mRNAs are produced by the viral polymerase through a stuttering mechanism (By similarity). Prevents the establishment of the cellular antiviral state by inhibiting TRIM25-mediated DDX58 ubiquitination, which normally triggers the antiviral transduction signal that leads to the activation of type I IFN genes by transcription factors like IRF3 and IRF7. Prevents human EIF2AK2/PKR activation, either by binding double-strand RNA, or by interacting directly with EIF2AK2/PKR. This function may be important at the very beginning of the infection, when NS1 is mainly present in the cytoplasm. Also binds poly(A) and U6 snRNA. Suppresses the RNA silencing-based antiviral response in Drosophila cells (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1.,Qin S, Liu Y, Tempel W, Eram MS, Bian C, Liu K, Senisterra G, Crombet L, Vedadi M, Min J Nat Commun. 2014 May 23;5:3952. doi: 10.1038/ncomms4952. PMID:24853335<ref>PMID:24853335</ref>		Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1.,Qin S, Liu Y, Tempel W, Eram MS, Bian C, Liu K, Senisterra G, Crombet L, Vedadi M, Min J Nat Commun. 2014 May 23;5:3952. doi: 10.1038/ncomms4952. PMID:24853335<ref>PMID:24853335</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 23:		Line 25:
	[[Category: DNA helicase]]		[[Category: DNA helicase]]
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Arrowsmith, C H.]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Bountra, C.]]	+	[[Category: Bountra, C]]
-	[[Category: Edwards, A M.]]	+	[[Category: Edwards, A M]]
-	[[Category: Min, J.]]	+	[[Category: Min, J]]
-	[[Category: Qin, S.]]	+	[[Category: Qin, S]]
-	[[Category: ~~SGC,~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Tempel, W.]]	+	[[Category: Tempel, W]]
-	[[Category: Xu, C.]]	+	[[Category: Xu, C]]
	[[Category: Chromodomain]]		[[Category: Chromodomain]]
	[[Category: Dna binding protein-viral protein complex]]		[[Category: Dna binding protein-viral protein complex]]
	[[Category: Sgc]]		[[Category: Sgc]]
-	[[Category: Structural genomic]]
-	[[Category: Structural genomics consortium]]
	[[Category: Viral]]		[[Category: Viral]]

OCA at 04:42, 4 June 2014

OCA — Wed, 04 Jun 2014 04:42:54 GMT

←Older revision		Revision as of 04:42, 4 June 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4o42\| PDB=4o42 \| SCENE= }}~~	+	==Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229==
-	===Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229===	+	<StructureSection load='4o42' size='340' side='right' caption='[[4o42]], [[Resolution\|resolution]] 1.87Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4o42]] 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=4O42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O42 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CHD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4o42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o42 RCSB], [http://www.ebi.ac.uk/pdbsum/4o42 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pathogens can interfere with vital biological processes of their host by mimicking host proteins. The NS1 protein of the influenza A H3N2 subtype possesses a histone H3K4-like sequence at its carboxyl terminus and has been reported to use this mimic to hijack host proteins. However, this mimic lacks a free N-terminus that is essential for binding to many known H3K4 readers. Here we show that the double chromodomains of CHD1 adopt an 'open pocket' to interact with the free N-terminal amine of H3K4, and the open pocket permits the NS1 mimic to bind in a distinct conformation. We also explored the possibility that NS1 hijacks other cellular proteins and found that the NS1 mimic has access to only a subset of chromatin-associated factors, such as WDR5. Moreover, methylation of the NS1 mimic can not be reversed by the H3K4 demethylase LSD1. Overall, we thus conclude that the NS1 mimic is an imperfect histone mimic.

-	~~==Function==~~	+	Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1.,Qin S, Liu Y, Tempel W, Eram MS, Bian C, Liu K, Senisterra G, Crombet L, Vedadi M, Min J Nat Commun. 2014 May 23;5:3952. doi: 10.1038/ncomms4952. PMID:24853335<ref>PMID:24853335</ref>
-	~~[[http://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component~~ of ~~the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription~~ by ~~RNA polymerase I, and more specifically the polymerase I transcription termination step~~. ~~Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling~~, ~~but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2~~, ~~the FACT complex~~, ~~the PAF complex as well as the U2 snRNP complex to H3K4me3~~. ~~Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3~~. ~~Required for maintaining open chromatin and pluripotency in embryonic stem cells~~.<ref>PMID:~~18042460~~</ref> [[http://www.uniprot.org/uniprot/NS1_I83A8 NS1_I83A8]] Inhibits post-transcriptional processing of cellular pre-mRNA, by binding and inhibiting two cellular proteins that are required for the 3'-end processing of cellular pre-mRNAs: the 30 kDa cleavage and polyadenylation specificity factor (CPSF4) and the poly(A)-binding protein 2 (PABPN1). This results in the accumulation of unprocessed 3' end pre-mRNAs which can't be exported from the nucleus. Cellular protein synthesis is thereby shut off very early after virus infection. Viral protein synthesis is not affected by the inhibition of the cellular 3' end processing machinery because the poly(A) tails of viral mRNAs are produced by the viral polymerase through a stuttering mechanism (By similarity). Prevents the establishment of the cellular antiviral state by inhibiting TRIM25-mediated DDX58 ubiquitination, which normally triggers the antiviral transduction signal that leads to the activation of type I IFN genes by transcription factors like IRF3 and IRF7. Prevents human EIF2AK2/PKR activation, either by binding double-strand RNA, or by interacting directly with EIF2AK2/PKR. This function may be important at the very beginning of the infection, when NS1 is mainly present in the cytoplasm. Also binds poly(A) and U6 snRNA. Suppresses the RNA silencing-based antiviral response in Drosophila cells (By similarity).	+

-	~~==About this Structure==~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4o42]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4O42 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA helicase]]		[[Category: DNA helicase]]
		+	[[Category: Human]]
	[[Category: Arrowsmith, C H.]]		[[Category: Arrowsmith, C H.]]
	[[Category: Bountra, C.]]		[[Category: Bountra, C.]]

OCA at 10:07, 16 April 2014

OCA — Wed, 16 Apr 2014 10:07:50 GMT

←Older revision		Revision as of 10:07, 16 April 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4o42\| PDB=4o42 \| SCENE= }}
		+	===Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229===

-	~~The entry 4o42~~ is ~~ON HOLD~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/CHD1_HUMAN CHD1_HUMAN]] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity (By similarity). Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells.<ref>PMID:18042460</ref> [[http://www.uniprot.org/uniprot/NS1_I83A8 NS1_I83A8]] Inhibits post-transcriptional processing of cellular pre-mRNA, by binding and inhibiting two cellular proteins that are required for the 3'-end processing of cellular pre-mRNAs: the 30 kDa cleavage and polyadenylation specificity factor (CPSF4) and the poly(A)-binding protein 2 (PABPN1). This results in the accumulation of unprocessed 3' end pre-mRNAs which can't be exported from the nucleus. Cellular protein synthesis is thereby shut off very early after virus infection. Viral protein synthesis is not affected by the inhibition of the cellular 3' end processing machinery because the poly(A) tails of viral mRNAs are produced by the viral polymerase through a stuttering mechanism (By similarity). Prevents the establishment of the cellular antiviral state by inhibiting TRIM25-mediated DDX58 ubiquitination, which normally triggers the antiviral transduction signal that leads to the activation of type I IFN genes by transcription factors like IRF3 and IRF7. Prevents human EIF2AK2/PKR activation, either by binding double-strand RNA, or by interacting directly with EIF2AK2/PKR. This function may be important at the very beginning of the infection, when NS1 is mainly present in the cytoplasm. Also binds poly(A) and U6 snRNA. Suppresses the RNA silencing-based antiviral response in Drosophila cells (By similarity).

-	~~Authors~~: ~~Qin, S., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C~~.~~, Edwards, A~~.M.~~, Min, J~~.~~, Structural Genomics Consortium (SGC)~~	+	==About this Structure==
		+	[[4o42]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O42 OCA].

-	~~Description~~: ~~Tandem chromodomains of human CHD1 in complex with influenza NS1~~ C-~~terminal tail dimethylated at K229~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: DNA helicase]]
		+	[[Category: Arrowsmith, C H.]]
		+	[[Category: Bountra, C.]]
		+	[[Category: Edwards, A M.]]
		+	[[Category: Min, J.]]
		+	[[Category: Qin, S.]]
		+	[[Category: SGC, Structural Genomics Consortium.]]
		+	[[Category: Tempel, W.]]
		+	[[Category: Xu, C.]]
		+	[[Category: Chromodomain]]
		+	[[Category: Dna binding protein-viral protein complex]]
		+	[[Category: Sgc]]
		+	[[Category: Structural genomic]]
		+	[[Category: Structural genomics consortium]]
		+	[[Category: Viral]]

OCA at 06:45, 22 January 2014

OCA — Wed, 22 Jan 2014 06:45:47 GMT

←Older revision		Revision as of 06:45, 22 January 2014
Line 3:		Line 3:
	The entry 4o42 is ON HOLD		The entry 4o42 is ON HOLD

-	Authors: Qin, S., Xu, C., Tempel, W., Arrowsmith,C.H., Bountra, C., Edwards, A.M., Min, J.~~, Structural Genomics Consortium~~, Structural Genomics Consortium (SGC)	+	Authors: Qin, S., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

	Description: Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229		Description: Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229

OCA: Protected "4o42" [edit=sysop:move=sysop]

OCA — Wed, 25 Dec 2013 09:33:18 GMT

Protected "4o42" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:33, 25 December 2013

OCA: New page: '''Unreleased structure''' The entry 4o42 is ON HOLD Authors: Qin, S., Xu, C., Tempel, W., Arrowsmith,C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium, Structur...

OCA — Wed, 25 Dec 2013 09:33:17 GMT

New page: '''Unreleased structure''' The entry 4o42 is ON HOLD Authors: Qin, S., Xu, C., Tempel, W., Arrowsmith,C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium, Structur...

New page

'''Unreleased structure'''

The entry 4o42 is ON HOLD

Authors: Qin, S., Xu, C., Tempel, W., Arrowsmith,C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium, Structural Genomics Consortium (SGC)

Description: Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229