6d84 - Revision history

OCA at 14:33, 13 March 2024

OCA — Wed, 13 Mar 2024 14:33:07 GMT

←Older revision		Revision as of 14:33, 13 March 2024
Line 3:		Line 3:
	<SX load='6d84' size='340' side='right' viewer='molstar' caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>		<SX load='6d84' size='340' side='right' viewer='molstar' caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human ~~Human~~] and [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6D84 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D84 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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">Electron Microscopy, [[Resolution\|Resolution]] 6.72Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nef ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), AP1B1, ADTB1, BAM22, CLAPB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), ARF1 ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=9606 HUMAN]), Ap1g1, Adtg, Clapg1 ([http:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])~~, ~~Ap1m1, Cltnm ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=10090 LK3 transgenic mice]), AP1S3 ([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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6d84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d84 OCA], [~~http~~://pdbe.org/6d84 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6d84 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6d84 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6d84 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=6d84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d84 OCA], [https://pdbe.org/6d84 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d84 RCSB], [https://www.ebi.ac.uk/pdbsum/6d84 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d84 ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/AP1S3_HUMAN AP1S3_HUMAN]] Acrodermatitis continua suppurativa of Hallopeau;Generalized pustular psoriasis;Pustulosis palmaris et plantaris. Disease susceptibility is associated with variations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~AP1S3_HUMAN AP1S3_HUMAN~~]] Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. Involved in TLR3 trafficking (PubMed:24791904).<ref>PMID:24791904</ref> [[http://www.uniprot.org/uniprot/AP1G1_MOUSE AP1G1_MOUSE]] Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. [[http://www.uniprot.org/uniprot/BST2_HUMAN BST2_HUMAN]] IFN-induced antiviral host restriction factor which efficiently blocks the release of diverse mammalian enveloped viruses by directly tethering nascent virions to the membranes of infected cells. Acts as a direct physical tether, holding virions to the cell membrane and linking virions to each other. The tethered virions can be internalized by endocytosis and subsequently degraded or they can remain on the cell surface. In either case, their spread as cell-free virions is restricted. Its target viruses belong to diverse families, including retroviridae: human immunodeficiency virus type 1 (HIV-1), human immunodeficiency virus type 2 (HIV-2), simian immunodeficiency viruses (SIVs), equine infectious anemia virus (EIAV), feline immunodeficiency virus (FIV), prototype foamy virus (PFV), Mason-Pfizer monkey virus (MPMV), human T-cell leukemia virus type 1 (HTLV-1), Rous sarcoma virus (RSV) and murine leukemia virus (MLV), flavivirideae: hepatitis C virus (HCV), filoviridae: ebola virus (EBOV) and marburg virus (MARV), arenaviridae: lassa virus (LASV) and machupo virus (MACV), herpesviridae: kaposis sarcoma-associated herpesvirus (KSHV), rhabdoviridae: vesicular stomatitis virus (VSV), orthomyxoviridae: influenza A virus, and paramyxoviridae: nipah virus. Can inhibit cell surface proteolytic activity of MMP14 causing decreased activation of MMP15 which results in inhibition of cell growth and migration. Can stimulate signaling by LILRA4/ILT7 and consequently provide negative feedback to the production of IFN by plasmacytoid dendritic cells in response to viral infection. Plays a role in the organization of the subapical actin cytoskeleton in polarized epithelial cells.<ref>PMID:18342597</ref> <ref>PMID:18200009</ref> <ref>PMID:19879838</ref> <ref>PMID:19564354</ref> <ref>PMID:19036818</ref> <ref>PMID:19179289</ref> <ref>PMID:20686043</ref> <ref>PMID:20943977</ref> <ref>PMID:20419159</ref> <ref>PMID:21529378</ref> <ref>PMID:21621240</ref> <ref>PMID:22065321</ref> <ref>PMID:22520941</ref> <ref>PMID:20399176</ref> <ref>PMID:20940320</ref> [[http://www.uniprot.org/uniprot/ARF1_HUMAN ARF1_HUMAN]] GTP-binding protein that functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP-ribosyltransferase. Involved in protein trafficking among different compartments. Modulates vesicle budding and uncoating within the Golgi complex. Deactivation induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, suggesting a crucial role in protein trafficking. In its GTP-bound form, its triggers the association with coat proteins with the Golgi membrane. The hydrolysis of ARF1-bound GTP, which is mediated by ARFGAPs proteins, is required for dissociation of coat proteins from Golgi membranes and vesicles. [[http://www.uniprot.org/uniprot/AP1B1_HUMAN AP1B1_HUMAN]] Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. [[http://www.uniprot.org/uniprot/AP1M1_MOUSE AP1M1_MOUSE]] Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the trans-Golgi network (TGN) and endosomes. The AP complexes mediate the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules.	+	[https://www.uniprot.org/uniprot/Q90VU7_9HIV1 Q90VU7_9HIV1] [https://www.uniprot.org/uniprot/BST2_HUMAN BST2_HUMAN] IFN-induced antiviral host restriction factor which efficiently blocks the release of diverse mammalian enveloped viruses by directly tethering nascent virions to the membranes of infected cells. Acts as a direct physical tether, holding virions to the cell membrane and linking virions to each other. The tethered virions can be internalized by endocytosis and subsequently degraded or they can remain on the cell surface. In either case, their spread as cell-free virions is restricted. Its target viruses belong to diverse families, including retroviridae: human immunodeficiency virus type 1 (HIV-1), human immunodeficiency virus type 2 (HIV-2), simian immunodeficiency viruses (SIVs), equine infectious anemia virus (EIAV), feline immunodeficiency virus (FIV), prototype foamy virus (PFV), Mason-Pfizer monkey virus (MPMV), human T-cell leukemia virus type 1 (HTLV-1), Rous sarcoma virus (RSV) and murine leukemia virus (MLV), flavivirideae: hepatitis C virus (HCV), filoviridae: ebola virus (EBOV) and marburg virus (MARV), arenaviridae: lassa virus (LASV) and machupo virus (MACV), herpesviridae: kaposis sarcoma-associated herpesvirus (KSHV), rhabdoviridae: vesicular stomatitis virus (VSV), orthomyxoviridae: influenza A virus, and paramyxoviridae: nipah virus. Can inhibit cell surface proteolytic activity of MMP14 causing decreased activation of MMP15 which results in inhibition of cell growth and migration. Can stimulate signaling by LILRA4/ILT7 and consequently provide negative feedback to the production of IFN by plasmacytoid dendritic cells in response to viral infection. Plays a role in the organization of the subapical actin cytoskeleton in polarized epithelial cells.<ref>PMID:18342597</ref> <ref>PMID:18200009</ref> <ref>PMID:19879838</ref> <ref>PMID:19564354</ref> <ref>PMID:19036818</ref> <ref>PMID:19179289</ref> <ref>PMID:20686043</ref> <ref>PMID:20943977</ref> <ref>PMID:20419159</ref> <ref>PMID:21529378</ref> <ref>PMID:21621240</ref> <ref>PMID:22065321</ref> <ref>PMID:22520941</ref> <ref>PMID:20399176</ref> <ref>PMID:20940320</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 A cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 A structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.	+
-		+
-	HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation.,Morris KL, Buffalo CZ, Sturzel CM, Heusinger E, Kirchhoff F, Ren X, Hurley JH Cell. 2018 Jul 26;174(3):659-671.e14. doi: 10.1016/j.cell.2018.07.004. PMID:30053425<ref>PMID:30053425</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6d84" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
	*[[Adaptin 3D structures\|Adaptin 3D structures]]		*[[Adaptin 3D structures\|Adaptin 3D structures]]
		+	*[[Protein Nef 3D structures\|Protein Nef 3D structures]]
		+	*[[Tetherin\|Tetherin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Human]]	+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Buffalo~~, C Z~~]]	+	[[Category: Buffalo CZ]]
-	[[Category: Hurley~~, J H~~]]	+	[[Category: Hurley JH]]
-	[[Category: Morris~~, K L]]~~	+	[[Category: Morris KL]]
-	~~[[Category: Ap]]~~	+
-	~~[[Category: Hiv]]~~	+
-	~~[[Category: Nef]]~~	+
-	~~[[Category: Protein transport]]~~	+
-	~~[[Category: Trafficking~~]]	+

OCA at 23:58, 10 April 2020

OCA — Fri, 10 Apr 2020 23:58:44 GMT

←Older revision		Revision as of 23:58, 10 April 2020
Line 3:		Line 3:
	<SX load='6d84' size='340' side='right' viewer='molstar' caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>		<SX load='6d84' size='340' side='right' viewer='molstar' caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6D84 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6D84 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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">nef ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), AP1B1, ADTB1, BAM22, CLAPB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), ARF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Ap1g1, Adtg, Clapg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Ap1m1, Cltnm ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), AP1S3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nef ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), AP1B1, ADTB1, BAM22, CLAPB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), ARF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Ap1g1, Adtg, Clapg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Ap1m1, Cltnm ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), AP1S3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6d84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d84 OCA], [http://pdbe.org/6d84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d84 RCSB], [http://www.ebi.ac.uk/pdbsum/6d84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d84 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=6d84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d84 OCA], [http://pdbe.org/6d84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d84 RCSB], [http://www.ebi.ac.uk/pdbsum/6d84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d84 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 20:52, 6 March 2020

OCA — Fri, 06 Mar 2020 20:52:01 GMT

←Older revision		Revision as of 20:52, 6 March 2020
Line 1:		Line 1:

	==Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer==		==Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer==
-	<~~StructureSection~~ load='6d84' size='340' side='right'caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>	+	<SX load='6d84' size='340' side='right' viewer='molstar' caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D84 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D84 FirstGlance]. <br>
Line 27:		Line 27:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Human]]		[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 10:01, 18 December 2019

OCA — Wed, 18 Dec 2019 10:01:11 GMT

←Older revision		Revision as of 10:01, 18 December 2019
Line 1:		Line 1:

	==Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer==		==Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer==
-	<StructureSection load='6d84' size='340' side='right' caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>	+	<StructureSection load='6d84' size='340' side='right'caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D84 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D84 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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">nef ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), AP1B1, ADTB1, BAM22, CLAPB2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), ARF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), Ap1g1, Adtg, Clapg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Ap1m1, Cltnm ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), AP1S3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6d84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d84 OCA], [http://pdbe.org/6d84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d84 RCSB], [http://www.ebi.ac.uk/pdbsum/6d84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d84 ProSAT]</span></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=6d84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d84 OCA], [http://pdbe.org/6d84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d84 RCSB], [http://www.ebi.ac.uk/pdbsum/6d84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d84 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6d84" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6d84" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adaptin 3D structures\|Adaptin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Buffalo, C Z]]		[[Category: Buffalo, C Z]]
	[[Category: Hurley, J H]]		[[Category: Hurley, J H]]

OCA at 21:49, 9 August 2018

OCA — Thu, 09 Aug 2018 21:49:19 GMT

←Older revision		Revision as of 21:49, 9 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6d84 is ~~ON HOLD~~	+	==Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer==
		+	<StructureSection load='6d84' size='340' side='right' caption='[[6d84]], [[Resolution\|resolution]] 6.72Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6d84]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D84 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D84 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6d84 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d84 OCA], [http://pdbe.org/6d84 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d84 RCSB], [http://www.ebi.ac.uk/pdbsum/6d84 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d84 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/AP1S3_HUMAN AP1S3_HUMAN]] Acrodermatitis continua suppurativa of Hallopeau;Generalized pustular psoriasis;Pustulosis palmaris et plantaris. Disease susceptibility is associated with variations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AP1S3_HUMAN AP1S3_HUMAN]] Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. Involved in TLR3 trafficking (PubMed:24791904).<ref>PMID:24791904</ref> [[http://www.uniprot.org/uniprot/AP1G1_MOUSE AP1G1_MOUSE]] Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. [[http://www.uniprot.org/uniprot/BST2_HUMAN BST2_HUMAN]] IFN-induced antiviral host restriction factor which efficiently blocks the release of diverse mammalian enveloped viruses by directly tethering nascent virions to the membranes of infected cells. Acts as a direct physical tether, holding virions to the cell membrane and linking virions to each other. The tethered virions can be internalized by endocytosis and subsequently degraded or they can remain on the cell surface. In either case, their spread as cell-free virions is restricted. Its target viruses belong to diverse families, including retroviridae: human immunodeficiency virus type 1 (HIV-1), human immunodeficiency virus type 2 (HIV-2), simian immunodeficiency viruses (SIVs), equine infectious anemia virus (EIAV), feline immunodeficiency virus (FIV), prototype foamy virus (PFV), Mason-Pfizer monkey virus (MPMV), human T-cell leukemia virus type 1 (HTLV-1), Rous sarcoma virus (RSV) and murine leukemia virus (MLV), flavivirideae: hepatitis C virus (HCV), filoviridae: ebola virus (EBOV) and marburg virus (MARV), arenaviridae: lassa virus (LASV) and machupo virus (MACV), herpesviridae: kaposis sarcoma-associated herpesvirus (KSHV), rhabdoviridae: vesicular stomatitis virus (VSV), orthomyxoviridae: influenza A virus, and paramyxoviridae: nipah virus. Can inhibit cell surface proteolytic activity of MMP14 causing decreased activation of MMP15 which results in inhibition of cell growth and migration. Can stimulate signaling by LILRA4/ILT7 and consequently provide negative feedback to the production of IFN by plasmacytoid dendritic cells in response to viral infection. Plays a role in the organization of the subapical actin cytoskeleton in polarized epithelial cells.<ref>PMID:18342597</ref> <ref>PMID:18200009</ref> <ref>PMID:19879838</ref> <ref>PMID:19564354</ref> <ref>PMID:19036818</ref> <ref>PMID:19179289</ref> <ref>PMID:20686043</ref> <ref>PMID:20943977</ref> <ref>PMID:20419159</ref> <ref>PMID:21529378</ref> <ref>PMID:21621240</ref> <ref>PMID:22065321</ref> <ref>PMID:22520941</ref> <ref>PMID:20399176</ref> <ref>PMID:20940320</ref> [[http://www.uniprot.org/uniprot/ARF1_HUMAN ARF1_HUMAN]] GTP-binding protein that functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP-ribosyltransferase. Involved in protein trafficking among different compartments. Modulates vesicle budding and uncoating within the Golgi complex. Deactivation induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, suggesting a crucial role in protein trafficking. In its GTP-bound form, its triggers the association with coat proteins with the Golgi membrane. The hydrolysis of ARF1-bound GTP, which is mediated by ARFGAPs proteins, is required for dissociation of coat proteins from Golgi membranes and vesicles. [[http://www.uniprot.org/uniprot/AP1B1_HUMAN AP1B1_HUMAN]] Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules. [[http://www.uniprot.org/uniprot/AP1M1_MOUSE AP1M1_MOUSE]] Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the trans-Golgi network (TGN) and endosomes. The AP complexes mediate the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 A cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 A structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.

-	~~Authors: Buffalo, C.Z~~., Morris, ~~K.L.~~, ~~Hurley~~, J.H.	+	HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation.,Morris KL, Buffalo CZ, Sturzel CM, Heusinger E, Kirchhoff F, Ren X, Hurley JH Cell. 2018 Jul 26;174(3):659-671.e14. doi: 10.1016/j.cell.2018.07.004. PMID:30053425<ref>PMID:30053425</ref>

-	~~Description: Structure~~ of the ~~cargo bound AP~~-1:~~Arf1~~:~~tetherin-Nef (L164A~~, ~~L165A) dileucine mutant dimer~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Morris, K.L]]	+	<div class="pdbe-citations 6d84" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Buffalo, C.Z~~]]	+	== References ==
-	[[Category: ~~Hurley, J.H~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Buffalo, C Z]]
		+	[[Category: Hurley, J H]]
		+	[[Category: Morris, K L]]
		+	[[Category: Ap]]
		+	[[Category: Hiv]]
		+	[[Category: Nef]]
		+	[[Category: Protein transport]]
		+	[[Category: Trafficking]]

OCA at 05:19, 18 July 2018

OCA — Wed, 18 Jul 2018 05:19:23 GMT

←Older revision		Revision as of 05:19, 18 July 2018
Line 5:		Line 5:
	Authors: Buffalo, C.Z., Morris, K.L., Hurley, J.H.		Authors: Buffalo, C.Z., Morris, K.L., Hurley, J.H.

-	Description: Structure of the ~~HIV~~-Nef (L164A, L165A) dileucine mutant ~~bound AP-1:Arf~~ dimer	+	Description: Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Morris, K.L]]		[[Category: Morris, K.L]]
	[[Category: Buffalo, C.Z]]		[[Category: Buffalo, C.Z]]
	[[Category: Hurley, J.H]]		[[Category: Hurley, J.H]]

OCA at 03:58, 20 June 2018

OCA — Wed, 20 Jun 2018 03:58:32 GMT

←Older revision		Revision as of 03:58, 20 June 2018
Line 5:		Line 5:
	Authors: Buffalo, C.Z., Morris, K.L., Hurley, J.H.		Authors: Buffalo, C.Z., Morris, K.L., Hurley, J.H.

-	Description: Structure of the HIV-Nef dileucine mutant bound AP-1:Arf dimer ~~monomeric subunit~~	+	Description: Structure of the HIV-Nef (L164A, L165A) dileucine mutant bound AP-1:Arf dimer
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Hurley, J.H]]
	[[Category: Morris, K.L]]		[[Category: Morris, K.L]]
	[[Category: Buffalo, C.Z]]		[[Category: Buffalo, C.Z]]
		+	[[Category: Hurley, J.H]]

OCA: Protected "6d84" [edit=sysop:move=sysop]

OCA — Wed, 02 May 2018 06:48:59 GMT

Protected "6d84" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:48, 2 May 2018

OCA: New page: '''Unreleased structure''' The entry 6d84 is ON HOLD Authors: Buffalo, C.Z., Morris, K.L., Hurley, J.H. Description: Structure of the HIV-Nef dileucine mutant bound AP-1:Arf dimer mono...

OCA — Wed, 02 May 2018 06:48:58 GMT

New page: '''Unreleased structure''' The entry 6d84 is ON HOLD Authors: Buffalo, C.Z., Morris, K.L., Hurley, J.H. Description: Structure of the HIV-Nef dileucine mutant bound AP-1:Arf dimer mono...

New page

'''Unreleased structure'''

The entry 6d84 is ON HOLD

Authors: Buffalo, C.Z., Morris, K.L., Hurley, J.H.

Description: Structure of the HIV-Nef dileucine mutant bound AP-1:Arf dimer monomeric subunit
[[Category: Unreleased Structures]]
[[Category: Hurley, J.H]]
[[Category: Morris, K.L]]
[[Category: Buffalo, C.Z]]