4h5i - Revision history

OCA at 08:01, 3 November 2022

OCA — Thu, 03 Nov 2022 08:01:13 GMT

←Older revision		Revision as of 08:01, 3 November 2022
Line 1:		Line 1:

	==Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)==		==Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)==
-	<StructureSection load='4h5i' size='340' side='right' caption='[[4h5i]], [[Resolution\|resolution]] 1.36Å' scene=''>	+	<StructureSection load='4h5i' size='340' side='right'caption='[[4h5i]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h5i]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H5I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4H5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h5i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H5I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4h5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h5i OCA], [https://pdbe.org/4h5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h5i RCSB], [https://www.ebi.ac.uk/pdbsum/4h5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h5i ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h5j\|4h5j]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SEC12, SED2, YNR026C, N3244 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=4h5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h5i OCA], [~~http~~://pdbe.org/4h5i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4h5i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4h5i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4h5i ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SEC12_YEAST SEC12_YEAST]] Guanine nucleotide-exchange factor (GEF) required for the formation or budding of transport vesicles from the ER. This function involves the cytoplasmic domain of the protein, which is thought to interact with the small GTP-binding protein SAR1. Required for autophagy.<ref>PMID:11694599</ref> <ref>PMID:12655150</ref> <ref>PMID:1327759</ref> <ref>PMID:16413259</ref> <ref>PMID:1649197</ref> <ref>PMID:1907973</ref> <ref>PMID:1907974</ref> <ref>PMID:1922074</ref> <ref>PMID:2512296</ref> <ref>PMID:3047151</ref> <ref>PMID:6996832</ref> <ref>PMID:7865879</ref> <ref>PMID:8106544</ref> <ref>PMID:8377826</ref> <ref>PMID:8583945</ref> <ref>PMID:9023343</ref>	+	[https://www.uniprot.org/uniprot/SEC12_YEAST SEC12_YEAST] Guanine nucleotide-exchange factor (GEF) required for the formation or budding of transport vesicles from the ER. This function involves the cytoplasmic domain of the protein, which is thought to interact with the small GTP-binding protein SAR1. Required for autophagy.<ref>PMID:11694599</ref> <ref>PMID:12655150</ref> <ref>PMID:1327759</ref> <ref>PMID:16413259</ref> <ref>PMID:1649197</ref> <ref>PMID:1907973</ref> <ref>PMID:1907974</ref> <ref>PMID:1922074</ref> <ref>PMID:2512296</ref> <ref>PMID:3047151</ref> <ref>PMID:6996832</ref> <ref>PMID:7865879</ref> <ref>PMID:8106544</ref> <ref>PMID:8377826</ref> <ref>PMID:8583945</ref> <ref>PMID:9023343</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 18824~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Hughson, F M~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Jeffrey, P D~~]]	+	[[Category: Hughson FM]]
-	[[Category: ~~McMahon, C~~]]	+	[[Category: Jeffrey PD]]
-	[[Category: ~~Beta propeller]]~~	+	[[Category: McMahon C]]
-	~~[[Category: Copii vesicle budding]]~~	+
-	~~[[Category: Potassium binding site]]~~	+
-	~~[[Category: Protein transport~~]]	+

OCA at 20:01, 15 December 2016

OCA — Thu, 15 Dec 2016 20:01:23 GMT

←Older revision		Revision as of 20:01, 15 December 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)==		==Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)==
	<StructureSection load='4h5i' size='340' side='right' caption='[[4h5i]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='4h5i' size='340' side='right' caption='[[4h5i]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H5I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H5I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h5j\|4h5j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h5j\|4h5j]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SEC12, SED2, YNR026C, N3244 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SEC12, SED2, YNR026C, N3244 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=4h5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h5i RCSB], [http://www.ebi.ac.uk/pdbsum/4h5i 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=4h5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h5i OCA], [http://pdbe.org/4h5i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h5i RCSB], [http://www.ebi.ac.uk/pdbsum/4h5i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h5i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SEC12_YEAST SEC12_YEAST]] Guanine nucleotide-exchange factor (GEF) required for the formation or budding of transport vesicles from the ER. This function involves the cytoplasmic domain of the protein, which is thought to interact with the small GTP-binding protein SAR1. Required for autophagy.<ref>PMID:11694599</ref> <ref>PMID:12655150</ref> <ref>PMID:1327759</ref> <ref>PMID:16413259</ref> <ref>PMID:1649197</ref> <ref>PMID:1907973</ref> <ref>PMID:1907974</ref> <ref>PMID:1922074</ref> <ref>PMID:2512296</ref> <ref>PMID:3047151</ref> <ref>PMID:6996832</ref> <ref>PMID:7865879</ref> <ref>PMID:8106544</ref> <ref>PMID:8377826</ref> <ref>PMID:8583945</ref> <ref>PMID:9023343</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 20:
	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 4h5i" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Hughson, F M]]		[[Category: Hughson, F M]]
	[[Category: Jeffrey, P D]]		[[Category: Jeffrey, P D]]

OCA at 09:38, 10 December 2014

OCA — Wed, 10 Dec 2014 09:38:16 GMT

←Older revision		Revision as of 09:38, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4h5i.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)==
		+	<StructureSection load='4h5i' size='340' side='right' caption='[[4h5i]], [[Resolution\|resolution]] 1.36Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4h5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H5I FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h5j\|4h5j]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SEC12, SED2, YNR026C, N3244 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=4h5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h5i RCSB], [http://www.ebi.ac.uk/pdbsum/4h5i PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	COPII-coated vesicles transport proteins and lipids from the endoplasmic reticulum to the Golgi. Crucial for the initiation of COPII coat assembly is Sec12, a guanine nucleotide exchange factor responsible for activating the small G protein Sar1. Once activated, Sar1/GTP binds to ER membranes and recruits COPII coat components (Sec23/24 and Sec13/31). Here, we report the 1.35 A resolution crystal structure of the catalytically active, 38-kDa cytoplasmic portion of Saccharomyces cerevisiae Sec12. Sec12 adopts a beta propeller fold. Conserved residues cluster around a loop we term the "K loop", which extends from the N-terminal propeller blade. Structure-guided site-directed mutagenesis, in conjunction with in vitro and in vivo functional studies, reveal that this region of Sec12 is catalytically essential, presumably because it makes direct contact with Sar1. Strikingly, the crystal structure also reveals that a single potassium ion stabilizes the K loop; bound potassium is, moreover, essential for optimum guanine nucleotide exchange activity in vitro. Thus, our results reveal a novel role for a potassium-stabilized loop in catalyzing guanine nucleotide exchange.

-	~~{{STRUCTURE_4h5i\| PDB=4h5i \| SCENE= }}~~	+	The Structure of Sec12 Implicates Potassium Ion Coordination in Sar1 Activation.,McMahon C, Studer SM, Clendinen C, Dann GP, Jeffrey PD, Hughson FM J Biol Chem. 2012 Oct 29. PMID:23109340<ref>PMID:23109340</ref>

-	~~===Crystal Structure~~ of the ~~Guanine Nucleotide Exchange Factor Sec12 (P1 form)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23109340}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4h5i]] is a 2 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H5I OCA].~~	+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Hughson, F M.]]	+	[[Category: Hughson, F M]]
-	[[Category: Jeffrey, P D.]]	+	[[Category: Jeffrey, P D]]
-	[[Category: McMahon, C.]]	+	[[Category: McMahon, C]]
	[[Category: Beta propeller]]		[[Category: Beta propeller]]
	[[Category: Copii vesicle budding]]		[[Category: Copii vesicle budding]]
	[[Category: Potassium binding site]]		[[Category: Potassium binding site]]
	[[Category: Protein transport]]		[[Category: Protein transport]]

OCA at 08:32, 9 January 2013

OCA — Wed, 09 Jan 2013 08:32:08 GMT

←Older revision		Revision as of 08:32, 9 January 2013
Line 5:		Line 5:
	===Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)===		===Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)===

		+	{{ABSTRACT_PUBMED_23109340}}

	==About this Structure==		==About this Structure==

OCA at 06:38, 14 November 2012

OCA — Wed, 14 Nov 2012 06:38:36 GMT

←Older revision		Revision as of 06:38, 14 November 2012
Line 1:		Line 1:
-	[[Image:4h5i.~~jpg~~\|left\|200px]]	+	[[Image:4h5i.png\|left\|200px]]

	{{STRUCTURE_4h5i\| PDB=4h5i \| SCENE= }}		{{STRUCTURE_4h5i\| PDB=4h5i \| SCENE= }}

OCA at 14:04, 8 November 2012

OCA — Thu, 08 Nov 2012 14:04:22 GMT

←Older revision		Revision as of 14:04, 8 November 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4h5i.jpg\|left\|200px]]

-	~~The entry~~ 4h5i ~~is ON HOLD~~	+	{{STRUCTURE_4h5i\| PDB=4h5i \| SCENE= }}

-	~~Authors: McMahon, C., Jeffrey, P.D., Hughson, F.M.~~	+	===Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)===

-	~~Description: Crystal~~ Structure ~~of the Guanine Nucleotide Exchange Factor Sec12~~	+
		+	==About this Structure==
		+	[[4h5i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H5I OCA].
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Hughson, F M.]]
		+	[[Category: Jeffrey, P D.]]
		+	[[Category: McMahon, C.]]
		+	[[Category: Beta propeller]]
		+	[[Category: Copii vesicle budding]]
		+	[[Category: Potassium binding site]]
		+	[[Category: Protein transport]]

OCA: Protected "4h5i" [edit=sysop:move=sysop]

OCA — Wed, 26 Sep 2012 20:13:12 GMT

Protected "4h5i" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:13, 26 September 2012

OCA: New page: '''Unreleased structure''' The entry 4h5i is ON HOLD Authors: McMahon, C., Jeffrey, P.D., Hughson, F.M. Description: Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12

OCA — Wed, 26 Sep 2012 20:13:11 GMT

New page: '''Unreleased structure''' The entry 4h5i is ON HOLD Authors: McMahon, C., Jeffrey, P.D., Hughson, F.M. Description: Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12

New page

'''Unreleased structure'''

The entry 4h5i is ON HOLD

Authors: McMahon, C., Jeffrey, P.D., Hughson, F.M.

Description: Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12