6qbw - Revision history

OCA at 11:57, 24 January 2024

OCA — Wed, 24 Jan 2024 11:57:33 GMT

←Older revision		Revision as of 11:57, 24 January 2024
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	<StructureSection load='6qbw' size='340' side='right'caption='[[6qbw]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6qbw' size='340' side='right'caption='[[6qbw]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qbw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Htlv~~-~~2 Htlv~~-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qbw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_T-lymphotropic_virus_2 Human T-lymphotropic virus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QBW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~pol ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=11909 HTLV-2])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qbw OCA], [https://pdbe.org/6qbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qbw RCSB], [https://www.ebi.ac.uk/pdbsum/6qbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qbw 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=6qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qbw OCA], [https://pdbe.org/6qbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qbw RCSB], [https://www.ebi.ac.uk/pdbsum/6qbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qbw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/POL_HTLV2 POL_HTLV2] The matrix domain targets Gag, Gag-Pro and Gag-Pro-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus.[UniProtKB:P03345] Matrix protein.[UniProtKB:P03345] Forms the spherical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.[UniProtKB:P03362] Binds strongly to viral nucleic acids and promote their aggregation. Also destabilizes the nucleic acids duplexes via highly structured zinc-binding motifs.[UniProtKB:P03345] The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell (Potential). Cleaves the translation initiation factor eIF4G leading to the inhibition of host cap-dependent translation (By similarity).[UniProtKB:P03362][PROSITE-ProRule:PRU00275] RT is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5'-endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA-Pro binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.<ref>PMID:8623556</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Htlv~~-2]]	+	[[Category: Human T-lymphotropic virus 2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barski~~, M S~~]]	+	[[Category: Barski MS]]
-	[[Category: Maertens~~, G N]]~~	+	[[Category: Maertens GN]]
-	~~[[Category: Deltaretrovirus]]~~	+
-	~~[[Category: Integration]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Retrovirus]]~~	+
-	~~[[Category: Strand-transfer]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:51, 14 April 2021

OCA — Wed, 14 Apr 2021 06:51:37 GMT

←Older revision		Revision as of 06:51, 14 April 2021
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	==Structure of the HTLV-2 integrase catalytic core domain in complex with calcium==		==Structure of the HTLV-2 integrase catalytic core domain in complex with calcium==
-	<StructureSection load='6qbw' size='340' side='right'caption='[[6qbw]]' scene=''>	+	<StructureSection load='6qbw' size='340' side='right'caption='[[6qbw]], [[Resolution\|resolution]] 2.40Å' 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=6QBW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6QBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qbw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Htlv-2 Htlv-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QBW 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=6qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qbw OCA], [~~http~~://pdbe.org/6qbw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qbw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qbw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qbw 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=CA:CALCIUM+ION'>CA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11909 HTLV-2])</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=6qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qbw OCA], [https://pdbe.org/6qbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qbw RCSB], [https://www.ebi.ac.uk/pdbsum/6qbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qbw ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus and the most oncogenic pathogen. Many of the ~20 million HTLV-1 infected people will develop severe leukaemia or an ALS-like motor disease, unless a therapy becomes available. A key step in the establishment of infection is the integration of viral genetic material into the host genome, catalysed by the retroviral integrase (IN) enzyme. Here, we use X-ray crystallography and single-particle cryo-electron microscopy to determine the structure of the functional deltaretroviral IN assembled on viral DNA ends and bound to the B56gamma subunit of its human host factor, protein phosphatase 2 A. The structure reveals a tetrameric IN assembly bound to two molecules of the phosphatase via a conserved short linear motif. Insight into the deltaretroviral intasome and its interaction with the host will be crucial for understanding the pattern of integration events in infected individuals and therefore bears important clinical implications.
		+
		+	Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56gamma.,Barski MS, Minnell JJ, Hodakova Z, Pye VE, Nans A, Cherepanov P, Maertens GN Nat Commun. 2020 Oct 7;11(1):5043. doi: 10.1038/s41467-020-18874-y. PMID:33028863<ref>PMID:33028863</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6qbw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Retroviral integrase 3D structures\|Retroviral integrase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Htlv-2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barski MS]]	+	[[Category: Barski, M S]]
-	[[Category: Maertens GN]]	+	[[Category: Maertens, G N]]
		+	[[Category: Deltaretrovirus]]
		+	[[Category: Integration]]
		+	[[Category: Nucleotidyltransferase]]
		+	[[Category: Retrovirus]]
		+	[[Category: Strand-transfer]]
		+	[[Category: Transferase]]

OCA at 07:04, 30 September 2020

OCA — Wed, 30 Sep 2020 07:04:47 GMT

←Older revision		Revision as of 07:04, 30 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6qbw ~~is ON HOLD until Paper Publication~~	+	==Structure of the HTLV-2 integrase catalytic core domain in complex with calcium==
-		+	<StructureSection load='6qbw' size='340' side='right'caption='[[6qbw]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6QBW 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=6qbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qbw OCA], [http://pdbe.org/6qbw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qbw RCSB], [http://www.ebi.ac.uk/pdbsum/6qbw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qbw ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Barski MS]]
		+	[[Category: Maertens GN]]

OCA at 07:23, 30 October 2019

OCA — Wed, 30 Oct 2019 07:23:39 GMT

←Older revision		Revision as of 07:23, 30 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 02 Jan 2019 05:03:20 GMT

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

←Older revision

Revision as of 05:03, 2 January 2019

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

OCA — Wed, 02 Jan 2019 05:03:19 GMT

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

New page

'''Unreleased structure'''

The entry 6qbw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]