3c1i - Revision history

OCA at 14:54, 1 November 2023

OCA — Wed, 01 Nov 2023 14:54:29 GMT

←Older revision		Revision as of 14:54, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3c1i' size='340' side='right'caption='[[3c1i]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3c1i' size='340' side='right'caption='[[3c1i]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C1I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C1I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>~~</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]] 2.3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1xqf\|1xqf]], [[1u7g\|1u7g]], [[2b2f\|2b2f]], [[3b9w\|3b9w]], [[3c1g\|3c1g]], [[3c1h\|3c1h]], [[3c1j\|3c1j]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">amtB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [https://pdbe.org/3c1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [https://www.ebi.ac.uk/pdbsum/3c1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c1i 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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [https://pdbe.org/3c1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [https://www.ebi.ac.uk/pdbsum/3c1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c1i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia.	+	[https://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI] Involved in the uptake of ammonia.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lupo, D]]	+	[[Category: Lupo D]]
-	[[Category: Winkler~~, F K]]~~	+	[[Category: Winkler FK]]
-	~~[[Category: Ammonia transport]]~~	+
-	~~[[Category: Amtb]]~~	+
-	~~[[Category: Inner membrane]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Phe-gate mutant]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 07:29, 10 November 2021

OCA — Wed, 10 Nov 2021 07:29:09 GMT

←Older revision		Revision as of 07:29, 10 November 2021
Line 1:		Line 1:

	==Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB==		==Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB==
-	<StructureSection load='3c1i' size='340' side='right' caption='[[3c1i]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3c1i' size='340' side='right'caption='[[3c1i]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3C1I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C1I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqf\|1xqf]], [[1u7g\|1u7g]], [[2b2f\|2b2f]], [[3b9w\|3b9w]], [[3c1g\|3c1g]], [[3c1h\|3c1h]], [[3c1j\|3c1j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xqf\|1xqf]], [[1u7g\|1u7g]], [[2b2f\|2b2f]], [[3b9w\|3b9w]], [[3c1g\|3c1g]], [[3c1h\|3c1h]], [[3c1j\|3c1j]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">amtB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">amtB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [~~http~~://pdbe.org/3c1i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3c1i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3c1i 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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [https://pdbe.org/3c1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [https://www.ebi.ac.uk/pdbsum/3c1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c1i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia.	+	[[https://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c1/3c1i_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c1/3c1i_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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 3c1i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3c1i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Lupo, D]]		[[Category: Lupo, D]]
	[[Category: Winkler, F K]]		[[Category: Winkler, F K]]

OCA at 08:16, 25 October 2017

OCA — Wed, 25 Oct 2017 08:16:18 GMT

←Older revision		Revision as of 08:16, 25 October 2017
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 3c1i" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3c1i" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ion channels\|Ion channels]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:25, 4 August 2016

OCA — Thu, 04 Aug 2016 22:25:35 GMT

←Older revision		Revision as of 22:25, 4 August 2016
Line 1:		Line 1:
		+
	==Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB==		==Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB==
	<StructureSection load='3c1i' size='340' side='right' caption='[[3c1i]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3c1i' size='340' side='right' caption='[[3c1i]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C1I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C1I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqf\|1xqf]], [[1u7g\|1u7g]], [[2b2f\|2b2f]], [[3b9w\|3b9w]], [[3c1g\|3c1g]], [[3c1h\|3c1h]], [[3c1j\|3c1j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqf\|1xqf]], [[1u7g\|1u7g]], [[2b2f\|2b2f]], [[3b9w\|3b9w]], [[3c1g\|3c1g]], [[3c1h\|3c1h]], [[3c1j\|3c1j]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">amtB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">amtB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [http://www.ebi.ac.uk/pdbsum/3c1i 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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [http://pdbe.org/3c1i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [http://www.ebi.ac.uk/pdbsum/3c1i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3c1i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=3c1i ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	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 3c1i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels\|Ion channels]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Lupo, D]]		[[Category: Lupo, D]]
	[[Category: Winkler, F K]]		[[Category: Winkler, F K]]

OCA at 13:37, 25 December 2014

OCA — Thu, 25 Dec 2014 13:37:54 GMT

←Older revision		Revision as of 13:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C1I FirstGlance]. <br>		<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C1I FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqf\|1xqf]], [[1u7g\|1u7g]], [[2b2f\|2b2f]], [[3b9w\|3b9w]], [[3c1g\|3c1g]], [[3c1h\|3c1h]], [[3c1j\|3c1j]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqf\|1xqf]], [[1u7g\|1u7g]], [[2b2f\|2b2f]], [[3b9w\|3b9w]], [[3c1g\|3c1g]], [[3c1h\|3c1h]], [[3c1j\|3c1j]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">amtB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">amtB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [http://www.ebi.ac.uk/pdbsum/3c1i 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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [http://www.ebi.ac.uk/pdbsum/3c1i PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Lupo, D.]]	+	[[Category: Lupo, D]]
-	[[Category: Winkler, F K.]]	+	[[Category: Winkler, F K]]
	[[Category: Ammonia transport]]		[[Category: Ammonia transport]]
	[[Category: Amtb]]		[[Category: Amtb]]

OCA at 21:33, 2 October 2014

OCA — Thu, 02 Oct 2014 21:33:59 GMT

←Older revision		Revision as of 21:33, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3c1i.~~png~~\|~~left~~\|200px]]	+	==Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB==
		+	<StructureSection load='3c1i' size='340' side='right' caption='[[3c1i]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3c1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C1I FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqf\|1xqf]], [[1u7g\|1u7g]], [[2b2f\|2b2f]], [[3b9w\|3b9w]], [[3c1g\|3c1g]], [[3c1h\|3c1h]], [[3c1j\|3c1j]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">amtB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3c1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c1i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c1i RCSB], [http://www.ebi.ac.uk/pdbsum/3c1i 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/c1/3c1i_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 conduction mechanism of Escherichia coli AmtB, the structurally and functionally best characterized representative of the ubiquitous Amt/Rh family, has remained controversial in several aspects. The predominant view has been that it facilitates the movement of ammonium in its uncharged form as indicated by the hydrophobic nature of a pore located in the center of each subunit of the homotrimer. Using site-directed mutagenesis and a combination of biochemical and crystallographic methods, we have investigated mechanistic questions concerning the putative periplasmic ammonium ion binding site S1 and the adjacent periplasmic "gate" formed by two highly conserved phenylalanine residues, F107 and F215. Our results challenge models that propose that NH(4)(+) deprotonation takes place at S1 before NH(3) conduction through the pore. The presence of S1 confers two critical features on AmtB, both essential for its function: ammonium scavenging efficiency at very low ammonium concentration and selectivity against water and physiologically important cations. We show that AmtB activity absolutely requires F215 but not F107 and that removal or obstruction of the phenylalanine gate produces an open but inactive channel. The phenyl ring of F215 must thus play a very specific role in promoting transfer and deprotonation of substrate from S1 to the central pore. We discuss these results with respect to three distinct mechanisms of conduction that have been considered so far. We conclude that substrate deprotonation is an essential part of the conduction mechanism, but we do not rule out net electrogenic transport.

-	~~{{STRUCTURE_3c1i\| PDB=3c1i \| SCENE= }}~~	+	Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB.,Javelle A, Lupo D, Ripoche P, Fulford T, Merrick M, Winkler FK Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5040-5. Epub 2008 Mar 24. PMID:18362341<ref>PMID:18362341</ref>

-	~~===Substrate binding~~, ~~deprotonation and selectivity at the periplasmic entrance~~ of the E. ~~coli ammonia channel AmtB===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18362341}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3c1i]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018362341<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Lupo, D.]]		[[Category: Lupo, D.]]

OCA: Protected "3c1i" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 21:07:24 GMT

Protected "3c1i" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:07, 7 January 2013

OCA at 21:07, 7 January 2013

OCA — Mon, 07 Jan 2013 21:07:19 GMT

←Older revision		Revision as of 21:07, 7 January 2013
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-	{{Seed}}
	[[Image:3c1i.png\|left\|200px]]		[[Image:3c1i.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3c1i", 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_3c1i\| PDB=3c1i \| SCENE= }}		{{STRUCTURE_3c1i\| PDB=3c1i \| SCENE= }}

	===Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB===		===Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18362341}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18362341 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18362341}}		{{ABSTRACT_PUBMED_18362341}}

	==About this Structure==		==About this Structure==
-	~~3C1I~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA].	+	[[3c1i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18362341~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018362341</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Lupo, D.]]		[[Category: Lupo, D.]]
Line 34:		Line 22:
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Transport protein]]		[[Category: Transport protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:36:54 2009''

OCA at 15:36, 17 February 2009

OCA — Tue, 17 Feb 2009 15:36:55 GMT

←Older revision		Revision as of 15:36, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3C1I is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA].	+	3C1I is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C1I OCA].

	==Reference==		==Reference==
-	Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB., Javelle A, Lupo D, Ripoche P, Fulford T, Merrick M, Winkler FK, Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5040-5. Epub 2008 Mar 24. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18362341 18362341]~~	+	<ref group="xtra">PMID:18362341</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Lupo, D.]]		[[Category: Lupo, D.]]
	[[Category: Winkler, F K.]]		[[Category: Winkler, F K.]]
Line 36:		Line 35:
	[[Category: Transport protein]]		[[Category: Transport protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 00~~:37:~~16 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:36:54 2009''

OCA at 21:37, 28 July 2008

OCA — Mon, 28 Jul 2008 21:37:19 GMT

←Older revision		Revision as of 21:37, 28 July 2008
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-	[[Image:3c1i.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3c1i.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3c1i\| PDB=3c1i \| SCENE= }}		{{STRUCTURE_3c1i\| PDB=3c1i \| SCENE= }}

-	~~'''~~Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB~~'''~~	+	===Substrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB===


-	~~==Overview==~~	+	<!--
-	The ~~conduction mechanism of Escherichia coli AmtB~~, ~~the structurally and functionally best characterized representative of the ubiquitous Amt/Rh family~~, ~~has remained controversial in several aspects. The predominant view has been that it facilitates~~ the ~~movement of ammonium in its uncharged form as indicated by~~ the hydrophobic nature of a pore located in the center of each subunit of the homotrimer. Using site-directed mutagenesis and a combination of biochemical and crystallographic methods, we have investigated mechanistic questions concerning the putative periplasmic ammonium ion binding site S1 and the adjacent periplasmic "gate" formed by two highly conserved phenylalanine residues, F107 and F215. Our results challenge models that propose that NH(~~4)(+) deprotonation takes place~~ at ~~S1 before NH(3) conduction through the pore. The presence of S1 confers two critical features on AmtB, both essential for its function~~: ~~ammonium scavenging efficiency at very low ammonium concentration and selectivity against water and physiologically important cations~~. ~~We show that AmtB activity absolutely requires F215 but not F107 and that removal or obstruction of the phenylalanine gate produces an open but inactive channel~~. The phenyl ring of F215 must thus play a very specific role in promoting transfer and deprotonation of substrate from S1 to the central pore. We discuss these results with respect to three distinct mechanisms of conduction that have been considered so far. We conclude that substrate deprotonation is ~~an essential part of~~ the ~~conduction mechanism, but we do not rule out net electrogenic transport~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18362341}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18362341 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18362341}}

	==About this Structure==		==About this Structure==
Line 31:		Line 35:
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Transport protein]]		[[Category: Transport protein]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Apr 16 23~~:09:56 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 00:37:16 2008''