6qbj - Revision history

OCA at 10:40, 15 November 2023

OCA — Wed, 15 Nov 2023 10:40:26 GMT

←Older revision		Revision as of 10:40, 15 November 2023
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	==Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics==		==Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics==
-	<StructureSection load='6qbj' size='340' side='right'caption='[[6qbj~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='6qbj' size='340' side='right'caption='[[6qbj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qbj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QBJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qbj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovine_alphaherpesvirus_1 Bovine alphaherpesvirus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QBJ FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=6qbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qbj OCA], [~~http~~://pdbe.org/6qbj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qbj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qbj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qbj ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</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=6qbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qbj OCA], [https://pdbe.org/6qbj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qbj RCSB], [https://www.ebi.ac.uk/pdbsum/6qbj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qbj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q89806_9ALPH Q89806_9ALPH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bovine alphaherpesvirus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Karska, N]]	+	[[Category: Karska N]]
-	[[Category: Rodziewicz-Motowidlo, S]]	+	[[Category: Rodziewicz-Motowidlo S]]
-	~~[[Category: Transmembrane protein]]~~	+
-	~~[[Category: Ul49 5 viral protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 13:45, 10 May 2019

OCA — Fri, 10 May 2019 13:45:01 GMT

←Older revision		Revision as of 13:45, 10 May 2019
Line 1:		Line 1:

	==Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics==		==Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics==
-	<StructureSection load='6qbj' size='340' side='right' caption='[[6qbj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='6qbj' size='340' side='right'caption='[[6qbj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6qbj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QBJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6qbj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QBJ FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Karska, N]]		[[Category: Karska, N]]
	[[Category: Rodziewicz-Motowidlo, S]]		[[Category: Rodziewicz-Motowidlo, S]]

OCA at 08:33, 6 March 2019

OCA — Wed, 06 Mar 2019 08:33:18 GMT

←Older revision		Revision as of 08:33, 6 March 2019
Line 1:		Line 1:

	==Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics==		==Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics==
-	<StructureSection load='6qbj' size='340' side='right' caption='[[6qbj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='6qbj' size='340' side='right' caption='[[6qbj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6qbj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QBJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6qbj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QBJ FirstGlance]. <br>

OCA at 15:36, 27 February 2019

OCA — Wed, 27 Feb 2019 15:36:16 GMT

←Older revision		Revision as of 15:36, 27 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qbj is ~~ON HOLD~~	+	==Structure determination of transmembrane- C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics==
		+	<StructureSection load='6qbj' size='340' side='right' caption='[[6qbj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6qbj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QBJ FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene></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=6qbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qbj OCA], [http://pdbe.org/6qbj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qbj RCSB], [http://www.ebi.ac.uk/pdbsum/6qbj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qbj ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The transporter associated with antigen processing (TAP) directly participates in the immune response as a key component of the cytosolic peptide to major histocompatibility complex (MHC) class I protein loading machinery. This makes TAP an important target for viruses avoiding recognition by CD8+ T lymphocytes. Its activity can be suppressed by the UL49.5 protein produced by bovine herpesvirus 1, although the mechanism of this inhibition has not been understood so far. Therefore, the main goal of our study was to investigate the 3D structure of bovine herpesvirus 1 - encoded UL49.5 protein. The final structure of the inhibitor was established using circular dichroism (CD), 2D nuclear magnetic resonance (NMR), and molecular dynamics (MD) in membrane mimetic environments. In NMR studies, UL49.5 was represented by two fragments: the extracellular region (residues 1-35) and the transmembrane-intracellular fragment (residues 36-75), displaying various functions during viral invasion. After the empirical structure determination, a molecular docking procedure was used to predict the complex of UL49.5 with the TAP heterodimer. Our results revealed that UL49.5 adopted a highly flexible membrane-proximal helical structure in the extracellular part. In the transmembrane region, we observed two short alpha-helices. Furthermore, the cytoplasmic part had an unordered structure. Finally, we propose three different orientations of UL49.5 in the complex with TAP. Our studies provide, for the first time, the experimental structural information on UL49.5 and structure-based insight in its mechanism of action which might be helpful in designing new drugs against viral infections.

-	~~Authors: Karska~~, N., Rodziewicz-Motowidlo, S.	+	Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics.,Karska N, Graul M, Sikorska E, Zhukov I, Slusarz MJ, Kasprzykowski F, Lipinska AD, Rodziewicz-Motowidlo S Biochim Biophys Acta Biomembr. 2019 Feb 14;1861(5):926-938. doi:, 10.1016/j.bbamem.2019.02.005. PMID:30772281<ref>PMID:30772281</ref>

-	~~Description: Structure determination~~ of ~~transmembrane-C-terminal fragment~~ of ~~UL49~~.~~5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Rodziewicz~~-~~Motowidlo, S]]~~	+	<div class="pdbe-citations 6qbj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Karska, N]]		[[Category: Karska, N]]
		+	[[Category: Rodziewicz-Motowidlo, S]]
		+	[[Category: Transmembrane protein]]
		+	[[Category: Ul49 5 viral protein]]
		+	[[Category: Viral protein]]

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

OCA — Wed, 02 Jan 2019 05:02:02 GMT

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

←Older revision

Revision as of 05:02, 2 January 2019

OCA: New page: '''Unreleased structure''' The entry 6qbj is ON HOLD Authors: Karska, N., Rodziewicz-Motowidlo, S. Description: Structure determination of transmembrane-C-terminal fragment of UL49.5 p...

OCA — Wed, 02 Jan 2019 05:02:00 GMT

New page: '''Unreleased structure''' The entry 6qbj is ON HOLD Authors: Karska, N., Rodziewicz-Motowidlo, S. Description: Structure determination of transmembrane-C-terminal fragment of UL49.5 p...

New page

'''Unreleased structure'''

The entry 6qbj is ON HOLD

Authors: Karska, N., Rodziewicz-Motowidlo, S.

Description: Structure determination of transmembrane-C-terminal fragment of UL49.5 protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics
[[Category: Unreleased Structures]]
[[Category: Rodziewicz-Motowidlo, S]]
[[Category: Karska, N]]