7dnu - Revision history

OCA at 16:36, 29 November 2023

OCA — Wed, 29 Nov 2023 16:36:57 GMT

←Older revision		Revision as of 16:36, 29 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7dnu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/African_swine_fever_virus_BA71V African swine fever virus BA71V]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DNU FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dnu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/African_swine_fever_virus_BA71V African swine fever virus BA71V]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DNU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</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]] 2.245Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</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=7dnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dnu OCA], [https://pdbe.org/7dnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dnu RCSB], [https://www.ebi.ac.uk/pdbsum/7dnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dnu 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=7dnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dnu OCA], [https://pdbe.org/7dnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dnu RCSB], [https://www.ebi.ac.uk/pdbsum/7dnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dnu ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:13, 28 December 2022

OCA — Wed, 28 Dec 2022 09:13:05 GMT

←Older revision		Revision as of 09:13, 28 December 2022
Line 1:		Line 1:

	==mRNA-decapping enzyme g5Rp with inhibitor insp6 complex==		==mRNA-decapping enzyme g5Rp with inhibitor insp6 complex==
-	<StructureSection load='7dnu' size='340' side='right'caption='[[7dnu]]' scene=''>	+	<StructureSection load='7dnu' size='340' side='right'caption='[[7dnu]], [[Resolution\|resolution]] 2.25Å' 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=7DNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DNU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dnu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/African_swine_fever_virus_BA71V African swine fever virus BA71V]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DNU 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=7dnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dnu OCA], [https://pdbe.org/7dnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dnu RCSB], [https://www.ebi.ac.uk/pdbsum/7dnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dnu 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=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</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=7dnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dnu OCA], [https://pdbe.org/7dnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dnu RCSB], [https://www.ebi.ac.uk/pdbsum/7dnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dnu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DIPP_ASFB7 DIPP_ASFB7] Decapping enzyme required for the removal of the 5'-end m7GpppN cap tethered to viral and host mRNAs to allow their decay in cells (PubMed:19695654). May therefore accelerate viral and cellular mRNA turnover to eliminate competing host mRNAs and allow stage-specific synthesis of viral proteins. Acceleration of the turnover of cellular transcripts may even promote the shutoff of host protein synthesis (PubMed:29021398). In addition to the mRNA cap, g5R also efficiently hydrolyzes diphosphoinositol polyphosphates. Down-regulation of the level of PP-InsP5 (diphosphoinositol pentakisphosphate) may play a role in viral manipulation of the cellular secretory pathway, a step necessary for the formation of virions (PubMed:11773415). Binds viral and cellular poly(A) mRNAs, thereby decreasing both types of mRNAs (PubMed:19695654, PubMed:29021398).<ref>PMID:11773415</ref> <ref>PMID:19695654</ref> <ref>PMID:29021398</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Removal of 5' cap on cellular mRNAs by the African swine fever virus (ASFV) decapping enzyme g5R protein (g5Rp) is beneficial to viral gene expression during the early stages of infection. As the only nucleoside diphosphate-linked moiety X (Nudix) decapping enzyme encoded in the ASFV genome, g5Rp works in both the degradation of cellular mRNA and the hydrolyzation of the diphosphoinositol polyphosphates. Here, we report the structures of dimeric g5Rp and its complex with inositol hexakisphosphate (InsP(6)). The two g5Rp protomers interact head to head to form a dimer, and the dimeric interface is formed by extensive polar and nonpolar interactions. Each protomer is composed of a unique N-terminal helical domain and a C-terminal classic Nudix domain. As g5Rp is an mRNA-decapping enzyme, we identified key residues, including K(8), K(94), K(95), K(98), K(175), R(221), and K(243) located on the substrate RNA binding interfaces of g5Rp which are important to RNA binding and decapping enzyme activity. Furthermore, the g5Rp-mediated mRNA decapping was inhibited by InsP(6). The g5Rp-InsP(6) complex structure showed that the InsP(6) molecules occupy the same regions that primarily mediate g5Rp-RNA interaction, elucidating the roles of InsP(6) in the regulation of the viral decapping activity of g5Rp in mRNA degradation. Collectively, these results provide the structural basis of interaction between RNA and g5Rp and highlight the inhibitory mechanism of InsP(6) on mRNA decapping by g5Rp. IMPORTANCE ASF is a highly contagious hemorrhagic viral disease in domestic pigs which causes high mortality. Currently, there are still no effective vaccines or specific drugs available against this particular virus. The protein g5Rp is the only viral mRNA-decapping enzyme, playing an essential role in the machinery assembly of mRNA regulation and translation initiation. In this study, we solved the crystal structures of g5Rp dimer and complex with InsP(6). Structure-based mutagenesis studies revealed critical residues involved in a candidate RNA binding region, which also play pivotal roles in complex with InsP(6). Notably, InsP(6) can inhibit g5Rp activity by competitively blocking the binding of substrate mRNA to the enzyme. Our structure-function studies provide the basis for potential anti-ASFV inhibitor designs targeting the critical enzyme.
		+
		+	Structural Insight into Molecular Inhibitory Mechanism of InsP(6) on African Swine Fever Virus mRNA-Decapping Enzyme g5Rp.,Yang Y, Zhang C, Li X, Li L, Chen Y, Yang X, Zhao Y, Chen C, Wang W, Zhong Z, Yang C, Huang Z, Su D J Virol. 2022 May 25;96(10):e0190521. doi: 10.1128/jvi.01905-21. Epub 2022 Apr , 28. PMID:35481780<ref>PMID:35481780</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dnu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: African swine fever virus BA71V]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen C]]		[[Category: Chen C]]

OCA at 16:46, 15 December 2021

OCA — Wed, 15 Dec 2021 16:46:28 GMT

←Older revision		Revision as of 16:46, 15 December 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7dnu is ~~ON HOLD until Paper Publication~~	+	==mRNA-decapping enzyme g5Rp with inhibitor insp6 complex==
-		+	<StructureSection load='7dnu' size='340' side='right'caption='[[7dnu]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DNU FirstGlance]. <br>
-	~~Description~~:	+	</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=7dnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dnu OCA], [https://pdbe.org/7dnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dnu RCSB], [https://www.ebi.ac.uk/pdbsum/7dnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dnu ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen C]]
		+	[[Category: Li L]]
		+	[[Category: Li XH]]
		+	[[Category: Su D]]
		+	[[Category: Yang Y]]

OCA at 04:27, 7 April 2021

OCA — Wed, 07 Apr 2021 04:27:13 GMT

←Older revision		Revision as of 04:27, 7 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dnu is ON HOLD	+	The entry 7dnu is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7dnu" [edit=sysop:move=sysop]

OCA — Wed, 16 Dec 2020 11:09:07 GMT

Protected "7dnu" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:09, 16 December 2020

OCA: New page: '''Unreleased structure''' The entry 7dnu is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 16 Dec 2020 11:09:06 GMT

New page: '''Unreleased structure''' The entry 7dnu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7dnu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]