3dl8 - Revision history

OCA at 09:41, 21 February 2024

2024-02-21T09:41:52Z

←Older revision		Revision as of 09:41, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3dl8' size='340' side='right'caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>		<StructureSection load='3dl8' size='340' side='right'caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex~~ aeolicus~~" huber and stetter 2001~~] and [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] and [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>secA, div+, BSU35300 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Vibrio subtilis~~" ~~Ehrenberg 1835]), secY~~, ~~aq_079 (~~[~~https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001~~]~~), secG, aq_098 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=63363 "Aquifex aeolicus" Huber and Stetter 2001])~~</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]] 7.5Å</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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [https://pdbe.org/3dl8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [https://www.ebi.ac.uk/pdbsum/3dl8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl8 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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [https://pdbe.org/3dl8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [https://www.ebi.ac.uk/pdbsum/3dl8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	~~[[https://www.uniprot.org/uniprot/SECG_AQUAE SECG_AQUAE]] Subunit of the protein translocation channel SecYEG. [~~[https://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU]] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] [[https://www.uniprot.org/uniprot/SECY_AQUAE SECY_AQUAE]] The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently (By similarity).	+	[https://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3dl8 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=3dl8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Most proteins are secreted from bacteria by the interaction of the cytoplasmic SecA ATPase with a membrane channel, formed by the heterotrimeric SecY complex. Here we report the crystal structure of SecA bound to the SecY complex, with a maximum resolution of 4.5 angstrom (A), obtained for components from Thermotoga maritima. One copy of SecA in an intermediate state of ATP hydrolysis is bound to one molecule of the SecY complex. Both partners undergo important conformational changes on interaction. The polypeptide-cross-linking domain of SecA makes a large conformational change that could capture the translocation substrate in a 'clamp'. Polypeptide movement through the SecY channel could be achieved by the motion of a 'two-helix finger' of SecA inside the cytoplasmic funnel of SecY, and by the coordinated tightening and widening of SecA's clamp above the SecY pore. SecA binding generates a 'window' at the lateral gate of the SecY channel and it displaces the plug domain, preparing the channel for signal sequence binding and channel opening.
-
-	Structure of a complex of the ATPase SecA and the protein-translocation channel.,Zimmer J, Nam Y, Rapoport TA Nature. 2008 Oct 16;455(7215):936-43. PMID:18923516<ref>PMID:18923516</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3dl8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Preprotein translocase\|Preprotein translocase]]	+	*[[Preprotein translocase 3D structures\|Preprotein translocase 3D structures]]
	*[[SecA\|SecA]]		*[[SecA\|SecA]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus ~~huber and stetter 2001~~]]	+	[[Category: Aquifex aeolicus]]
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nam, Y]]	+	[[Category: Nam Y]]
-	[[Category: Rapoport~~, T A~~]]	+	[[Category: Rapoport TA]]
-	[[Category: Zimmer, J]]	+	[[Category: Zimmer J]]
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Protein transport]]~~	+
-	~~[[Category: Reca-type atpase membrane protein translocation protein-protein complex]]~~	+
-	~~[[Category: Translocation]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 08:01, 9 February 2022

2022-02-09T08:01:34Z

←Older revision		Revision as of 08:01, 9 February 2022
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	==Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA==		==Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA==
-	<StructureSection load='3dl8' size='340' side='right' caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>	+	<StructureSection load='3dl8' size='340' side='right'caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001] and [~~http~~://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001] and [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">secA, div+, BSU35300 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), secY, aq_079 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001]), secG, aq_098 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">secA, div+, BSU35300 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), secY, aq_079 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001]), secG, aq_098 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [~~http~~://pdbe.org/3dl8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dl8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl8 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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [https://pdbe.org/3dl8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [https://www.ebi.ac.uk/pdbsum/3dl8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SECG_AQUAE SECG_AQUAE]] Subunit of the protein translocation channel SecYEG. [[~~http~~://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU]] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] [[~~http~~://www.uniprot.org/uniprot/SECY_AQUAE SECY_AQUAE]] The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently (By similarity).	+	[[https://www.uniprot.org/uniprot/SECG_AQUAE SECG_AQUAE]] Subunit of the protein translocation channel SecYEG. [[https://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU]] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] [[https://www.uniprot.org/uniprot/SECY_AQUAE SECY_AQUAE]] The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Nam, Y]]		[[Category: Nam, Y]]
	[[Category: Rapoport, T A]]		[[Category: Rapoport, T A]]

OCA at 09:48, 14 November 2018

2018-11-14T09:48:12Z

←Older revision		Revision as of 09:48, 14 November 2018
Line 1:		Line 1:
		+
	==Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA==		==Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA==
	<StructureSection load='3dl8' size='340' side='right' caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>		<StructureSection load='3dl8' size='340' side='right' caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001] and [http://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001] and [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">secA, div+, BSU35300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~]), secY, aq_079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001]), secG, aq_098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">secA, div+, BSU35300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), secY, aq_079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001]), secG, aq_098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [http://pdbe.org/3dl8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl8 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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [http://pdbe.org/3dl8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dl8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dl8_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 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Nam, Y]]		[[Category: Nam, Y]]
	[[Category: Rapoport, T A]]		[[Category: Rapoport, T A]]

OCA at 05:11, 10 February 2016

2016-02-10T05:11:02Z

←Older revision		Revision as of 05:11, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3dl8' size='340' side='right' caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>		<StructureSection load='3dl8' size='340' side='right' caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aquifex_aeolicus Aquifex~~ aeolicus] and [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001] and [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">secA, div+, BSU35300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~]), secY, aq_079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus]), secG, aq_098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">secA, div+, BSU35300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900]), secY, aq_079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001]), secG, aq_098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl8 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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [http://pdbe.org/3dl8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=3dl8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3dl8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus]]	+	[[Category: Aquifex aeolicus huber and stetter 2001]]
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Nam, Y]]		[[Category: Nam, Y]]
	[[Category: Rapoport, T A]]		[[Category: Rapoport, T A]]

OCA at 12:02, 25 December 2014

2014-12-25T12:02:14Z

←Older revision		Revision as of 12:02, 25 December 2014
Line 6:		Line 6:
	<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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl8 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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl8 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SECG_AQUAE SECG_AQUAE]] Subunit of the protein translocation channel SecYEG. [[http://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU]] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] [[http://www.uniprot.org/uniprot/SECY_AQUAE SECY_AQUAE]] The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:05, 18 December 2014

2014-12-18T14:05:36Z

←Older revision		Revision as of 14:05, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3dl8\| PDB=3dl8 \| SCENE= }}~~	+	==Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA==
-	===Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA===	+	<StructureSection load='3dl8' size='340' side='right' caption='[[3dl8]], [[Resolution\|resolution]] 7.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18923516}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dl8]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] and [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL8 FirstGlance]. <br>
		+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">secA, div+, BSU35300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis]), secY, aq_079 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus]), secG, aq_098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</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=3dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl8 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl8 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/dl/3dl8_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 ==
		+	Most proteins are secreted from bacteria by the interaction of the cytoplasmic SecA ATPase with a membrane channel, formed by the heterotrimeric SecY complex. Here we report the crystal structure of SecA bound to the SecY complex, with a maximum resolution of 4.5 angstrom (A), obtained for components from Thermotoga maritima. One copy of SecA in an intermediate state of ATP hydrolysis is bound to one molecule of the SecY complex. Both partners undergo important conformational changes on interaction. The polypeptide-cross-linking domain of SecA makes a large conformational change that could capture the translocation substrate in a 'clamp'. Polypeptide movement through the SecY channel could be achieved by the motion of a 'two-helix finger' of SecA inside the cytoplasmic funnel of SecY, and by the coordinated tightening and widening of SecA's clamp above the SecY pore. SecA binding generates a 'window' at the lateral gate of the SecY channel and it displaces the plug domain, preparing the channel for signal sequence binding and channel opening.

-	~~==Function==~~	+	Structure of a complex of the ATPase SecA and the protein-translocation channel.,Zimmer J, Nam Y, Rapoport TA Nature. 2008 Oct 16;455(7215):936-43. PMID:18923516<ref>PMID:18923516</ref>
-	~~[[http://www.uniprot.org/uniprot/SECG_AQUAE SECG_AQUAE]] Subunit~~ of ~~the protein translocation channel SecYEG. [[http://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU]] Part of the Sec protein translocase~~ complex~~. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis~~ of ~~ATP to~~ the ~~transfer of proteins into~~ and ~~across~~ the ~~cell membrane, serving as an ATP~~-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] [[http://www.uniprot.org/uniprot/SECY_AQUAE SECY_AQUAE]] The central subunit of the protein translocation channel ~~SecYEG~~. ~~Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7~~, ~~and are clamped together by SecE at the back~~. ~~The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix~~ (~~helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently (By similarity~~).	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3dl8]] is~~ a ~~8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aquifex_aeolicus Aquifex aeolicus] and [http://en~~.~~wikipedia.org~~/~~wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Preprotein translocase\|Preprotein translocase]]		*[[Preprotein translocase\|Preprotein translocase]]
	*[[SecA\|SecA]]		*[[SecA\|SecA]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:018923516</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Nam, Y.]]	+	[[Category: Nam, Y]]
-	[[Category: Rapoport, T A.]]	+	[[Category: Rapoport, T A]]
-	[[Category: Zimmer, J.]]	+	[[Category: Zimmer, J]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]

OCA at 06:54, 29 September 2013

2013-09-29T06:54:55Z

←Older revision		Revision as of 06:54, 29 September 2013
Line 1:		Line 1:
-	[[Image:3dl8.png\|left\|200px]]
-
	{{STRUCTURE_3dl8\| PDB=3dl8 \| SCENE= }}		{{STRUCTURE_3dl8\| PDB=3dl8 \| SCENE= }}
-
	===Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA===		===Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA===
		+	{{ABSTRACT_PUBMED_18923516}}

-	~~{{ABSTRACT_PUBMED_18923516}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/SECG_AQUAE SECG_AQUAE]] Subunit of the protein translocation channel SecYEG. [[http://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU]] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] [[http://www.uniprot.org/uniprot/SECY_AQUAE SECY_AQUAE]] The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently (By similarity).

	==About this Structure==		==About this Structure==
Line 11:		Line 10:

	==See Also==		==See Also==
		+	*[[Preprotein translocase\|Preprotein translocase]]
	*[[SecA\|SecA]]		*[[SecA\|SecA]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:018923516</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018923516</ref><references group="xtra"/><references/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]

OCA at 16:26, 20 October 2012

2012-10-20T16:26:42Z

←Older revision		Revision as of 16:26, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3dl8]] is a 8 chain structure ~~of [[SecA]]~~ with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] and [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA].	+	[[3dl8]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] and [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA].

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

OCA: Protected "3dl8" [edit=sysop:move=sysop]

2012-07-26T21:43:15Z

Protected "3dl8" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:43, 26 July 2012

OCA at 21:43, 26 July 2012

2012-07-26T21:43:14Z

←Older revision		Revision as of 21:43, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3dl8.png\|left\|200px]]		[[Image:3dl8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dl8", 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_3dl8\| PDB=3dl8 \| SCENE= }}		{{STRUCTURE_3dl8\| PDB=3dl8 \| SCENE= }}

	===Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA===		===Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18923516}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18923516 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18923516}}		{{ABSTRACT_PUBMED_18923516}}

	==About this Structure==		==About this Structure==
-	~~3DL8~~ is a 8 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] and [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA].	+	[[3dl8]] is a 8 chain structure of [[SecA]] with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] and [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL8 OCA].
		+
		+	==See Also==
		+	*[[SecA\|SecA]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18923516~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018923516</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
Line 31:		Line 22:
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
-	[[Category: Cytoplasm]]
	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
Line 40:		Line 30:
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Transport]]		[[Category: Transport]]
-	[[Category: Zinc]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:54:56 2010''