1yd8 - Revision history

OCA at 08:56, 14 February 2024

OCA — Wed, 14 Feb 2024 08:56:39 GMT

←Older revision		Revision as of 08:56, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1yd8' size='340' side='right'caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1yd8' size='340' side='right'caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~] and [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GGA3~~, ~~KIAA0154 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])~~</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]] 2.8Å</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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [~~http~~://pdbe.org/1yd8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yd8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd8 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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [https://pdbe.org/1yd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~GGA3_HUMAN GGA3_HUMAN~~]~~] Plays~~ a ~~role in~~ protein ~~sorting and trafficking between~~ the ~~trans~~-~~Golgi network~~ (~~TGN~~) and ~~endosomes. Mediates~~ the ~~ARF~~-~~dependent recruitment of clathrin~~ to the ~~TGN and binds ubiquitinated proteins and membrane cargo molecules with a cytosolic acidic cluster~~-~~dileucine~~ (AC-LL) ~~motif~~.~~<ref>PMID:11301005</ref>~~	+	[https://www.uniprot.org/uniprot/UBC_BOVIN UBC_BOVIN] Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yd8 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yd8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Golgi-localized, gamma-ear-containing, Arf (ADP-ribosylation factor)-binding (GGA) proteins are clathrin adaptors that mediate the sorting of transmembrane-cargo molecules at the trans-Golgi network and endosomes. Cargo proteins can be directed into the GGA pathway by at least two different types of sorting signals: acidic cluster-dileucine motifs and covalent modification by ubiquitin. The latter modification is recognized by the GGAs through binding to their GAT [GGA and TOM (target of Myb)] domain. Here we report the crystal structure of the GAT domain of human GGA3 in a 1:1 complex with ubiquitin at 2.8-A resolution. Ubiquitin binds to a hydrophobic and acidic patch on helices alpha1 and alpha2 of the GAT three-helix bundle that includes Asn-223, Leu-227, Glu-230, Met-231, Asp-244, Glu-246, Leu-247, Glu-250, and Leu-251. The GAT-binding surface on ubiquitin is a hydrophobic patch centered on Ile-44 that is also responsible for binding most other ubiquitin effectors. The ubiquitin-binding site observed in the crystal is distinct from the Rabaptin-5-binding site on helices alpha2 and alpha3 of the GAT domain. Mutational analysis and modeling of the ubiquitin-Rabaptin-5-GAT ternary complex indicates that ubiquitin and Rabaptin-5 can bind to the GAT domain at two different sites without any steric conflict. This ability highlights the GAT domain as a hub for interactions with multiple partners in trafficking.
-
-	Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding proteins.,Prag G, Lee S, Mattera R, Arighi CN, Beach BM, Bonifacino JS, Hurley JH Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2334-9. Epub 2005 Feb 8. PMID:15701688<ref>PMID:15701688</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1yd8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[~~Ubiquitin~~\|~~Ubiquitin~~]]	+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bovin~~]]	+	[[Category: Bos taurus]]
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arighi~~, C N~~]]	+	[[Category: Arighi CN]]
-	[[Category: Beach~~, B M~~]]	+	[[Category: Beach BM]]
-	[[Category: Bonifacino~~, J S~~]]	+	[[Category: Bonifacino JS]]
-	[[Category: Hurley~~, J H~~]]	+	[[Category: Hurley JH]]
-	[[Category: Lee, S]]	+	[[Category: Lee S]]
-	[[Category: Mattera, R]]	+	[[Category: Mattera R]]
-	[[Category: Prag, G]]	+	[[Category: Prag G]]
-	~~[[Category: Chromosomal protein]]~~	+
-	~~[[Category: Mono-ubiquitination]]~~	+
-	~~[[Category: Post translational modification]]~~	+
-	~~[[Category: Protein transport]]~~	+
-	~~[[Category: Trafficking~~]]	+

OCA at 08:43, 20 January 2021

OCA — Wed, 20 Jan 2021 08:43:44 GMT

←Older revision		Revision as of 08:43, 20 January 2021
Line 1:		Line 1:

	==COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN==		==COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN==
-	<StructureSection load='1yd8' size='340' side='right' caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1yd8' size='340' side='right'caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://pdbe.org/1yd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd8 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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://pdbe.org/1yd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd8_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1yd8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1yd8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin\|Ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	[[Category: Bovin]]		[[Category: Bovin]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arighi, C N]]		[[Category: Arighi, C N]]
	[[Category: Beach, B M]]		[[Category: Beach, B M]]

OCA at 15:42, 12 October 2017

OCA — Thu, 12 Oct 2017 15:42:04 GMT

←Older revision		Revision as of 15:42, 12 October 2017
Line 1:		Line 1:
		+
	==COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN==		==COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN==
	<StructureSection load='1yd8' size='340' side='right' caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1yd8' size='340' side='right' caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bos_taurus Bos taurus~~] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://pdbe.org/1yd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum]</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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://pdbe.org/1yd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1yd8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1yd8" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ubiquitin\|Ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bos taurus~~]]	+	[[Category: Bovin]]
	[[Category: Human]]		[[Category: Human]]
	[[Category: Arighi, C N]]		[[Category: Arighi, C N]]

OCA at 00:50, 8 February 2016

OCA — Mon, 08 Feb 2016 00:50:33 GMT

←Older revision		Revision as of 00:50, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yd8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:20, 10 September 2015

OCA — Thu, 10 Sep 2015 06:20:50 GMT

←Older revision		Revision as of 06:20, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1yd8' size='340' side='right' caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1yd8' size='340' side='right' caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum]</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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://pdbe.org/1yd8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1yd8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Arighi, C N]]		[[Category: Arighi, C N]]
	[[Category: Beach, B M]]		[[Category: Beach, B M]]

OCA at 19:21, 24 December 2014

OCA — Wed, 24 Dec 2014 19:21:20 GMT

←Older revision		Revision as of 19:21, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum]</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=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GGA3_HUMAN GGA3_HUMAN]] Plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes. Mediates the ARF-dependent recruitment of clathrin to the TGN and binds ubiquitinated proteins and membrane cargo molecules with a cytosolic acidic cluster-dileucine (AC-LL) motif.<ref>PMID:11301005</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Arighi, C N.]]	+	[[Category: Arighi, C N]]
-	[[Category: Beach, B M.]]	+	[[Category: Beach, B M]]
-	[[Category: Bonifacino, J S.]]	+	[[Category: Bonifacino, J S]]
-	[[Category: Hurley, J H.]]	+	[[Category: Hurley, J H]]
-	[[Category: Lee, S.]]	+	[[Category: Lee, S]]
-	[[Category: Mattera, R.]]	+	[[Category: Mattera, R]]
-	[[Category: Prag, G.]]	+	[[Category: Prag, G]]
	[[Category: Chromosomal protein]]		[[Category: Chromosomal protein]]
	[[Category: Mono-ubiquitination]]		[[Category: Mono-ubiquitination]]

OCA at 21:48, 28 September 2014

OCA — Sun, 28 Sep 2014 21:48:04 GMT

←Older revision		Revision as of 21:48, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1yd8.~~png\|left~~\|200px]]	+	==COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN==
		+	<StructureSection load='1yd8' size='340' side='right' caption='[[1yd8]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YD8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GGA3, KIAA0154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yd8 RCSB], [http://www.ebi.ac.uk/pdbsum/1yd8 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd8_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Golgi-localized, gamma-ear-containing, Arf (ADP-ribosylation factor)-binding (GGA) proteins are clathrin adaptors that mediate the sorting of transmembrane-cargo molecules at the trans-Golgi network and endosomes. Cargo proteins can be directed into the GGA pathway by at least two different types of sorting signals: acidic cluster-dileucine motifs and covalent modification by ubiquitin. The latter modification is recognized by the GGAs through binding to their GAT [GGA and TOM (target of Myb)] domain. Here we report the crystal structure of the GAT domain of human GGA3 in a 1:1 complex with ubiquitin at 2.8-A resolution. Ubiquitin binds to a hydrophobic and acidic patch on helices alpha1 and alpha2 of the GAT three-helix bundle that includes Asn-223, Leu-227, Glu-230, Met-231, Asp-244, Glu-246, Leu-247, Glu-250, and Leu-251. The GAT-binding surface on ubiquitin is a hydrophobic patch centered on Ile-44 that is also responsible for binding most other ubiquitin effectors. The ubiquitin-binding site observed in the crystal is distinct from the Rabaptin-5-binding site on helices alpha2 and alpha3 of the GAT domain. Mutational analysis and modeling of the ubiquitin-Rabaptin-5-GAT ternary complex indicates that ubiquitin and Rabaptin-5 can bind to the GAT domain at two different sites without any steric conflict. This ability highlights the GAT domain as a hub for interactions with multiple partners in trafficking.

-	~~{{STRUCTURE_1yd8\| PDB=1yd8 \| SCENE= }}~~	+	Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding proteins.,Prag G, Lee S, Mattera R, Arighi CN, Beach BM, Bonifacino JS, Hurley JH Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2334-9. Epub 2005 Feb 8. PMID:15701688<ref>PMID:15701688</ref>

-	~~===COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15701688}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1yd8]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bos_taurus Bos taurus] and [http://en~~.~~wikipedia.org~~/~~wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA].~~	+

	==See Also==		==See Also==
	*[[Ubiquitin\|Ubiquitin]]		*[[Ubiquitin\|Ubiquitin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015701688<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 08:21, 20 October 2012

OCA — Sat, 20 Oct 2012 08:21:09 GMT

←Older revision		Revision as of 08:21, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1yd8]] is a 4 chain structure ~~of [[Ubiquitin]]~~ with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA].	+	[[1yd8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD8 OCA].

	==See Also==		==See Also==

OCA at 19:15, 25 July 2012

OCA — Wed, 25 Jul 2012 19:15:52 GMT

←Older revision		Revision as of 19:15, 25 July 2012
Line 1:		Line 1:
	[[Image:1yd8.png\|left\|200px]]		[[Image:1yd8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yd8", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1yd8\| PDB=1yd8 \| SCENE= }}		{{STRUCTURE_1yd8\| PDB=1yd8 \| SCENE= }}

	===COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN===		===COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15701688}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15701688 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15701688}}		{{ABSTRACT_PUBMED_15701688}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Ubiquitin]]	+	*[[Ubiquitin\|Ubiquitin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15701688~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015701688</ref><references group="xtra"/>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA: Protected "1yd8" [edit=sysop:move=sysop]

OCA — Sun, 26 Dec 2010 22:51:43 GMT

Protected "1yd8" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:51, 26 December 2010