6l5o - Revision history

OCA at 10:45, 27 March 2024

OCA — Wed, 27 Mar 2024 10:45:32 GMT

←Older revision		Revision as of 10:45, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6l5o' size='340' side='right'caption='[[6l5o]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6l5o' size='340' side='right'caption='[[6l5o]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6l5o]] is a 1 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=6L5O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6L5O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6l5o]] is a 1 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=6L5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L5O FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~DDX21 ([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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13]~~ </~~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=6l5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l5o OCA], [https://pdbe.org/6l5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l5o RCSB], [https://www.ebi.ac.uk/pdbsum/6l5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l5o ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6l5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l5o OCA], [~~http~~://pdbe.org/6l5o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6l5o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6l5o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6l5o ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DDX21_HUMAN DDX21_HUMAN]] RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77' (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292).<ref>PMID:11823437</ref> <ref>PMID:14559904</ref> <ref>PMID:18180292</ref> <ref>PMID:25260534</ref> <ref>PMID:25470060</ref> <ref>PMID:25477391</ref> <ref>PMID:9461305</ref>	+	[https://www.uniprot.org/uniprot/DDX21_HUMAN DDX21_HUMAN] RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77' (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292).<ref>PMID:11823437</ref> <ref>PMID:14559904</ref> <ref>PMID:18180292</ref> <ref>PMID:25260534</ref> <ref>PMID:25470060</ref> <ref>PMID:25477391</ref> <ref>PMID:9461305</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	RNA helicase DDX21 plays vital roles in ribosomal RNA biogenesis, transcription, and the regulation of host innate immunity during virus infection. How DDX21 recognizes and unwinds RNA and how DDX21 interacts with virus remain poorly understood. Here, crystal structures of human DDX21 determined in three distinct states are reported, including the apo-state, the AMPPNP plus single-stranded RNA (ssRNA) bound pre-hydrolysis state, and the ADP-bound post-hydrolysis state, revealing an open to closed conformational change upon RNA binding and unwinding. The core of the RNA unwinding machinery of DDX21 includes one wedge helix, one sensor motif V and the DEVD box, which links the binding pockets of ATP and ssRNA. The mutant D339H/E340G dramatically increases RNA binding activity. Moreover, Hill coefficient analysis reveals that DDX21 unwinds double-stranded RNA (dsRNA) in a cooperative manner. Besides, the nonstructural (NS1) protein of influenza A inhibits the ATPase and unwinding activity of DDX21 via small RNAs, which cooperatively assemble with DDX21 and NS1. The structures illustrate the dynamic process of ATP hydrolysis and RNA unwinding for RNA helicases, and the RNA modulated interaction between NS1 and DDX21 generates a fresh perspective toward the virus-host interface. It would benefit in developing therapeutics to combat the influenza virus infection.	+

-	Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation.,Chen Z, Li Z, Hu X, Xie F, Kuang S, Zhan B, Gao W, Chen X, Gao S, Li Y, Wang Y, Qian F, Ding C, Gan J, Ji C, Xu XW, Zhou Z, Huang J, He HH, Li J Adv Sci (Weinh). 2020 Jun 8;7(14):2000532. doi: 10.1002/advs.202000532., eCollection 2020 Jul. PMID:32714761<ref>PMID:32714761</ref>	+	==See Also==
-		+	*[[Helicase 3D structures\|Helicase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6l5o" 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: RNA helicase]]~~	+	[[Category: Chen ZJ]]
-	[[Category: Chen~~, Z J~~]]	+	[[Category: Hu XJ]]
-	[[Category: Hu~~, X J~~]]	+	[[Category: Li JX]]
-	[[Category: Li~~, J X~~]]	+	[[Category: Zhou Z]]
-	[[Category: Zhou, Z]]	+
-	~~[[Category: Adp bound complex]]~~	+
-	~~[[Category: Rna binding protein~~]]	+

OCA at 09:56, 12 August 2020

OCA — Wed, 12 Aug 2020 09:56:10 GMT

←Older revision		Revision as of 09:56, 12 August 2020
Line 1:		Line 1:

	==Crystal structure of human DEAD-box RNA helicase DDX21 at post-hydrolysis state==		==Crystal structure of human DEAD-box RNA helicase DDX21 at post-hydrolysis state==
-	<StructureSection load='6l5o' size='340' side='right'caption='[[6l5o]]' scene=''>	+	<StructureSection load='6l5o' size='340' side='right'caption='[[6l5o]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L5O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6L5O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6l5o]] is a 1 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=6L5O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6L5O FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6l5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l5o OCA], [http://pdbe.org/6l5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l5o RCSB], [http://www.ebi.ac.uk/pdbsum/6l5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l5o ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDX21 ([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/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6l5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l5o OCA], [http://pdbe.org/6l5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l5o RCSB], [http://www.ebi.ac.uk/pdbsum/6l5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l5o ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDX21_HUMAN DDX21_HUMAN]] RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77' (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292).<ref>PMID:11823437</ref> <ref>PMID:14559904</ref> <ref>PMID:18180292</ref> <ref>PMID:25260534</ref> <ref>PMID:25470060</ref> <ref>PMID:25477391</ref> <ref>PMID:9461305</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA helicase DDX21 plays vital roles in ribosomal RNA biogenesis, transcription, and the regulation of host innate immunity during virus infection. How DDX21 recognizes and unwinds RNA and how DDX21 interacts with virus remain poorly understood. Here, crystal structures of human DDX21 determined in three distinct states are reported, including the apo-state, the AMPPNP plus single-stranded RNA (ssRNA) bound pre-hydrolysis state, and the ADP-bound post-hydrolysis state, revealing an open to closed conformational change upon RNA binding and unwinding. The core of the RNA unwinding machinery of DDX21 includes one wedge helix, one sensor motif V and the DEVD box, which links the binding pockets of ATP and ssRNA. The mutant D339H/E340G dramatically increases RNA binding activity. Moreover, Hill coefficient analysis reveals that DDX21 unwinds double-stranded RNA (dsRNA) in a cooperative manner. Besides, the nonstructural (NS1) protein of influenza A inhibits the ATPase and unwinding activity of DDX21 via small RNAs, which cooperatively assemble with DDX21 and NS1. The structures illustrate the dynamic process of ATP hydrolysis and RNA unwinding for RNA helicases, and the RNA modulated interaction between NS1 and DDX21 generates a fresh perspective toward the virus-host interface. It would benefit in developing therapeutics to combat the influenza virus infection.
		+
		+	Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation.,Chen Z, Li Z, Hu X, Xie F, Kuang S, Zhan B, Gao W, Chen X, Gao S, Li Y, Wang Y, Qian F, Ding C, Gan J, Ji C, Xu XW, Zhou Z, Huang J, He HH, Li J Adv Sci (Weinh). 2020 Jun 8;7(14):2000532. doi: 10.1002/advs.202000532., eCollection 2020 Jul. PMID:32714761<ref>PMID:32714761</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6l5o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen ZJ]]	+	[[Category: RNA helicase]]
-	[[Category: Hu XJ]]	+	[[Category: Chen, Z J]]
-	[[Category: Li JX]]	+	[[Category: Hu, X J]]
-	[[Category: Zhou Z]]	+	[[Category: Li, J X]]
		+	[[Category: Zhou, Z]]
		+	[[Category: Adp bound complex]]
		+	[[Category: Rna binding protein]]

OCA at 10:07, 17 June 2020

OCA — Wed, 17 Jun 2020 10:07:50 GMT

←Older revision		Revision as of 10:07, 17 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6l5o is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of human DEAD-box RNA helicase DDX21 at post-hydrolysis state==
-		+	<StructureSection load='6l5o' size='340' side='right'caption='[[6l5o]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L5O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6L5O FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6l5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l5o OCA], [http://pdbe.org/6l5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l5o RCSB], [http://www.ebi.ac.uk/pdbsum/6l5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l5o ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen ZJ]]
		+	[[Category: Hu XJ]]
		+	[[Category: Li JX]]
		+	[[Category: Zhou Z]]

OCA at 05:01, 6 November 2019

OCA — Wed, 06 Nov 2019 05:01:05 GMT

←Older revision		Revision as of 05:01, 6 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6l5o is ON HOLD	+	The entry 6l5o is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6l5o" [edit=sysop:move=sysop]

OCA — Wed, 30 Oct 2019 07:22:05 GMT

Protected "6l5o" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:22, 30 October 2019

OCA: New page: '''Unreleased structure''' The entry 6l5o is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 30 Oct 2019 07:22:04 GMT

New page: '''Unreleased structure''' The entry 6l5o is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6l5o is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]