7kbc - Revision history

OCA at 15:20, 18 October 2023

OCA — Wed, 18 Oct 2023 15:20:40 GMT

←Older revision		Revision as of 15:20, 18 October 2023
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	<StructureSection load='7kbc' size='340' side='right'caption='[[7kbc]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='7kbc' size='340' side='right'caption='[[7kbc]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7kbc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~9infa 9infa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kbc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus Influenza A virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KBC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E4Z:Baloxavir+acid'>E4Z</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=QQ4:Hexa+Vinylpyrrolidone+K15'>QQ4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.25Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7kaf\|7kaf]], [[7k0w\|7k0w]], [[6w5p\|6w5p]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E4Z:Baloxavir+acid'>E4Z</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=QQ4:Hexa+Vinylpyrrolidone+K15'>QQ4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA-X ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11320 9INFA])~~</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=7kbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kbc OCA], [https://pdbe.org/7kbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kbc RCSB], [https://www.ebi.ac.uk/pdbsum/7kbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kbc 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=7kbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kbc OCA], [https://pdbe.org/7kbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kbc RCSB], [https://www.ebi.ac.uk/pdbsum/7kbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kbc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A5J6VBC3_9INFA A0A5J6VBC3_9INFA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Influenza A virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cuypers~~, M G~~]]	+	[[Category: Cuypers MG]]
-	[[Category: Kumar, G]]	+	[[Category: Kumar G]]
-	[[Category: Slavish, J]]	+	[[Category: Slavish J]]
-	[[Category: White~~, S W]]~~	+	[[Category: White SW]]
-	~~[[Category: Cleaved]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Influenza]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 15:03, 3 March 2021

OCA — Wed, 03 Mar 2021 15:03:27 GMT

←Older revision		Revision as of 15:03, 3 March 2021
Line 1:		Line 1:

	==The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D (construct with truncated loop 51-72) in complex with baloxavir acid==		==The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D (construct with truncated loop 51-72) in complex with baloxavir acid==
-	<StructureSection load='7kbc' size='340' side='right'caption='[[7kbc]]' scene=''>	+	<StructureSection load='7kbc' size='340' side='right'caption='[[7kbc]], [[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=7KBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KBC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kbc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/9infa 9infa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KBC 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=7kbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kbc OCA], [https://pdbe.org/7kbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kbc RCSB], [https://www.ebi.ac.uk/pdbsum/7kbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kbc 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=E4Z:Baloxavir+acid'>E4Z</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=QQ4:Hexa+Vinylpyrrolidone+K15'>QQ4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7kaf\|7kaf]], [[7k0w\|7k0w]], [[6w5p\|6w5p]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA-X ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11320 9INFA])</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=7kbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kbc OCA], [https://pdbe.org/7kbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kbc RCSB], [https://www.ebi.ac.uk/pdbsum/7kbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kbc ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. The anti-influenza drug baloxavir is highly effective, but is associated with resistance mutations that threaten its clinical efficacy. The endonuclease resides within the N-terminal domain of the PA subunit (PAN) of the influenza RNA dependent RNA polymerase, and we report here complexes of PAN with RNA and DNA oligonucleotides to understand its specificity and the structural basis of baloxavir resistance mutations. The RNA and DNA oligonucleotides bind within the substrate binding groove of PAN in a similar fashion, explaining the ability of the enzyme to cleave both substrates. The individual nucleotides occupy adjacent conserved pockets that flank the two-metal active site. However, the 2' OH of the RNA ribose moieties engage in additional interactions that appear to optimize the binding and cleavage efficiency for the natural substrate. The major baloxavir resistance mutation at position 38 is at the core of the substrate binding site, but structural studies and modeling suggest that it maintains the necessary virus fitness via compensating interactions with RNA. These studies will facilitate the development of new influenza therapeutics that spatially match the substrate and are less likely to elicit resistance mutations.
		+
		+	Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.,Kumar G, Cuypers M, Webby RR, Webb TR, White SW Nucleic Acids Res. 2021 Jan 19. pii: 6104438. doi: 10.1093/nar/gkaa1294. PMID:33469660<ref>PMID:33469660</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kbc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cuypers MG]]	+	[[Category: Cuypers, M G]]
-	[[Category: Kumar G]]	+	[[Category: Kumar, G]]
-	[[Category: Slavish J]]	+	[[Category: Slavish, J]]
-	[[Category: White SW]]	+	[[Category: White, S W]]
		+	[[Category: Cleaved]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Influenza]]
		+	[[Category: Nuclease]]
		+	[[Category: Viral protein]]

OCA at 11:11, 3 February 2021

OCA — Wed, 03 Feb 2021 11:11:51 GMT

←Older revision		Revision as of 11:11, 3 February 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7kbc is ON HOLD until Oct 02 2022~~	+	==The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D (construct with truncated loop 51-72) in complex with baloxavir acid==
-		+	<StructureSection load='7kbc' size='340' side='right'caption='[[7kbc]]' scene=''>
-	~~Authors: Cuypers, M.G., Kumar, G., Slavish, J., White, S.W.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KBC FirstGlance]. <br>
-	~~Description:~~ The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D (construct with truncated loop 51-72) in complex with baloxavir acid	+	</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=7kbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kbc OCA], [https://pdbe.org/7kbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kbc RCSB], [https://www.ebi.ac.uk/pdbsum/7kbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kbc ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Slavish~~, J]]	+	__TOC__
-	[[Category: ~~White, S.W~~]]	+	</StructureSection>
-	[[Category: Kumar, G]]	+	[[Category: Large Structures]]
-	[[Category: ~~Cuypers, M.G~~]]	+	[[Category: Cuypers MG]]
		+	[[Category: Kumar G]]
		+	[[Category: Slavish J]]
		+	[[Category: White SW]]

OCA at 06:29, 11 November 2020

OCA — Wed, 11 Nov 2020 06:29:31 GMT

←Older revision		Revision as of 06:29, 11 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kbc is ON HOLD	+	The entry 7kbc is ON HOLD until Oct 02 2022

	Authors: Cuypers, M.G., Kumar, G., Slavish, J., White, S.W.		Authors: Cuypers, M.G., Kumar, G., Slavish, J., White, S.W.

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

OCA — Wed, 07 Oct 2020 04:53:22 GMT

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

←Older revision

Revision as of 04:53, 7 October 2020

OCA: New page: '''Unreleased structure''' The entry 7kbc is ON HOLD Authors: Cuypers, M.G., Kumar, G., Slavish, J., White, S.W. Description: The crystal structure of the 2009/H1N1/California PA endon...

OCA — Wed, 07 Oct 2020 04:53:21 GMT

New page: '''Unreleased structure''' The entry 7kbc is ON HOLD Authors: Cuypers, M.G., Kumar, G., Slavish, J., White, S.W. Description: The crystal structure of the 2009/H1N1/California PA endon...

New page

'''Unreleased structure'''

The entry 7kbc is ON HOLD

Authors: Cuypers, M.G., Kumar, G., Slavish, J., White, S.W.

Description: The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D (construct with truncated loop 51-72) in complex with baloxavir acid
[[Category: Unreleased Structures]]
[[Category: Slavish, J]]
[[Category: White, S.W]]
[[Category: Kumar, G]]
[[Category: Cuypers, M.G]]