3rko - Revision history

OCA at 09:43, 1 March 2024

OCA — Fri, 01 Mar 2024 09:43:27 GMT

←Older revision		Revision as of 09:43, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3rko' size='340' side='right'caption='[[3rko]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3rko' size='340' side='right'caption='[[3rko]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Escherichia_coli~~ Escherichia coli]. The December 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Complex I'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. The December 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Complex I'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA7:7~~-~~CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>~~, ~~<scene name='pdbligand=LFA:EICOSANE'>LFA</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]] 3Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[https~~:~~//en.wikipedia.org/wiki/NADH:ubiquinone_reductase_(H(+)~~-~~translocating) NADH:ubiquinone reductase (H(~~+)-~~translocating)], with EC number [https://www.brenda~~-~~enzymes.info~~/~~php/result_flat.php4?ecno~~=~~1.6.5.3 1.6.5.3]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA7:7-CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</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=3rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rko OCA], [https://pdbe.org/3rko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rko RCSB], [https://www.ebi.ac.uk/pdbsum/3rko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rko 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=3rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rko OCA], [https://pdbe.org/3rko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rko RCSB], [https://www.ebi.ac.uk/pdbsum/3rko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NUOK_ECOBD NUOK_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01456] [[https://www.uniprot.org/uniprot/C6E9S6_ECOBD C6E9S6_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_00445] [[https://www.uniprot.org/uniprot/C6E9R4_ECOBD C6E9R4_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain.[RuleBase:RU003639] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01394]	+	[https://www.uniprot.org/uniprot/NUOK_ECOBD NUOK_ECOBD] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01456]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 A resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.	+
-		+
-	~~Structure of the membrane domain of respiratory complex I.,Efremov RG, Sazanov LA Nature. 2011 Aug 7. doi: 10.1038/nature10330. PMID:21822288<ref>PMID:21822288</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3rko" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[NADH-quinone oxidoreductase\|NADH-quinone oxidoreductase]]		*[[NADH-quinone oxidoreductase\|NADH-quinone oxidoreductase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Complex I]]		[[Category: Complex I]]
-	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: Efremov~~, R G~~]]	+	[[Category: Efremov RG]]
-	[[Category: Sazanov~~, L A]]~~	+	[[Category: Sazanov LA]]
-	~~[[Category: Complex i]]~~	+
-	~~[[Category: Cytoplasmic membrane]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Nadh]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Proton pump]]~~	+
-	~~[[Category: Ubiquinone~~]]	+

OCA at 10:14, 22 June 2022

OCA — Wed, 22 Jun 2022 10:14:49 GMT

←Older revision		Revision as of 10:14, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution==		==Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution==
-	<StructureSection load='3rko' size='340' side='right' caption='[[3rko]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='3rko' size='340' side='right'caption='[[3rko]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2011 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Complex I'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RKO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Complex I'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA7:7-CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA7:7-CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/NADH:ubiquinone_reductase_(H(+)-translocating) NADH:ubiquinone reductase (H(+)-translocating)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.3 1.6.5.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/NADH:ubiquinone_reductase_(H(+)-translocating) NADH:ubiquinone reductase (H(+)-translocating)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.3 1.6.5.3] </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=3rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rko OCA], [~~http~~://pdbe.org/3rko PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rko RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rko PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rko 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=3rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rko OCA], [https://pdbe.org/3rko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rko RCSB], [https://www.ebi.ac.uk/pdbsum/3rko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NUOK_ECOBD NUOK_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01456] [[~~http~~://www.uniprot.org/uniprot/C6E9S6_ECOBD C6E9S6_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_00445] [[~~http~~://www.uniprot.org/uniprot/C6E9R4_ECOBD C6E9R4_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain.[RuleBase:RU003639] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01394]	+	[[https://www.uniprot.org/uniprot/NUOK_ECOBD NUOK_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01456] [[https://www.uniprot.org/uniprot/C6E9S6_ECOBD C6E9S6_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_00445] [[https://www.uniprot.org/uniprot/C6E9R4_ECOBD C6E9R4_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain.[RuleBase:RU003639] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01394]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 28:
	[[Category: Complex I]]		[[Category: Complex I]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Efremov, R G]]		[[Category: Efremov, R G]]

OCA at 22:46, 5 August 2016

OCA — Fri, 05 Aug 2016 22:46:44 GMT

←Older revision		Revision as of 22:46, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution==		==Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution==
	<StructureSection load='3rko' size='340' side='right' caption='[[3rko]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3rko' size='340' side='right' caption='[[3rko]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Complex I'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RKO FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Complex I'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RKO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA7:7-CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA7:7-CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~NADH_dehydrogenase_~~(~~ubiquinone~~) NADH ~~dehydrogenase (~~ubiquinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.3 1.6.5.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NADH:ubiquinone_reductase_(H(+)-translocating) NADH:ubiquinone reductase (H(+)-translocating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.3 1.6.5.3] </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=3rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rko RCSB], [http://www.ebi.ac.uk/pdbsum/3rko 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=3rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rko OCA], [http://pdbe.org/3rko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rko RCSB], [http://www.ebi.ac.uk/pdbsum/3rko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 3rko" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NADH-quinone oxidoreductase\|NADH-quinone oxidoreductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:31, 25 December 2014

OCA — Thu, 25 Dec 2014 06:31:31 GMT

←Older revision		Revision as of 06:31, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3rko.~~png~~\|~~left\|200px~~]]	+	==Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution==
		+	<StructureSection load='3rko' size='340' side='right' caption='[[3rko]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rko]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Complex I'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RKO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA7:7-CYCLOHEXYLHEPTYL+4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>CA7</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NADH_dehydrogenase_(ubiquinone) NADH dehydrogenase (ubiquinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.3 1.6.5.3] </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=3rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rko RCSB], [http://www.ebi.ac.uk/pdbsum/3rko PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NUOK_ECOBD NUOK_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01456] [[http://www.uniprot.org/uniprot/C6E9S6_ECOBD C6E9S6_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_00445] [[http://www.uniprot.org/uniprot/C6E9R4_ECOBD C6E9R4_ECOBD]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain.[RuleBase:RU003639] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.[HAMAP-Rule:MF_01394]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 A resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.

-	~~<!--~~	+	Structure of the membrane domain of respiratory complex I.,Efremov RG, Sazanov LA Nature. 2011 Aug 7. doi: 10.1038/nature10330. PMID:21822288<ref>PMID:21822288</ref>
-	~~The line below this paragraph, containing "STRUCTURE_3rko", 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_3rko\| PDB=3rko \| SCENE= }}~~	+

-	~~===Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21822288}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on~~ PubMed ~~at http://www.pubmed.gov)~~, ~~where 21822288 is the PubMed ID number.~~	+	</StructureSection>
-	~~-->~~	+
-	~~{{ABSTRACT_PUBMED_21822288}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3rko]] is~~ a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the ~~Month] feature on ''Complex I'' by David Goodsell is [http://dx~~.~~doi~~.~~org/10~~.~~2210~~/~~rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021822288<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Complex I]]		[[Category: Complex I]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: Efremov, R G.]]	+	[[Category: Efremov, R G]]
-	[[Category: Sazanov, L A.]]	+	[[Category: Sazanov, L A]]
	[[Category: Complex i]]		[[Category: Complex i]]
	[[Category: Cytoplasmic membrane]]		[[Category: Cytoplasmic membrane]]

OCA at 04:46, 25 March 2012

OCA — Sun, 25 Mar 2012 04:46:29 GMT

←Older revision		Revision as of 04:46, 25 March 2012
Line 19:		Line 19:

	==About this Structure==		==About this Structure==
-	[[3rko]] is a 12 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=3RKO OCA].	+	[[3rko]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Complex I'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_12 10.2210/rcsb_pdb/mom_2011_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKO OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:021822288</ref><references group="xtra"/>		<ref group="xtra">PMID:021822288</ref><references group="xtra"/>
		+	[[Category: Complex I]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Efremov, R G.]]		[[Category: Efremov, R G.]]
	[[Category: Sazanov, L A.]]		[[Category: Sazanov, L A.]]

OCA at 06:17, 17 August 2011

OCA — Wed, 17 Aug 2011 06:17:24 GMT

←Older revision		Revision as of 06:17, 17 August 2011
Line 1:		Line 1:
-	[[Image:3rko.~~jpg~~\|left\|200px]]	+	[[Image:3rko.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution===		===Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21822288}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21822288 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21822288}}

	==About this Structure==		==About this Structure==
	[[3rko]] is a 12 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=3RKO OCA].		[[3rko]] is a 12 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=3RKO OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021822288</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Efremov, R G.]]		[[Category: Efremov, R G.]]

OCA at 09:00, 3 August 2011

OCA — Wed, 03 Aug 2011 09:00:29 GMT

←Older revision		Revision as of 09:00, 3 August 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3rko.jpg\|left\|200px]]

-	The ~~entry 3rko~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rko", 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_3rko\| PDB=3rko \| SCENE= }}

-	~~Authors: Efremov, R~~.~~G., Sazanov, L.A~~.	+	===Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution===

-	~~Description: Crystal~~ structure ~~of the membrane domain of respiratory complex I~~ from E. coli ~~at 3~~.~~0 angstrom resolution~~	+
		+	==About this Structure==
		+	[[3rko]] is a 12 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=3RKO OCA].
		+	[[Category: Escherichia coli]]
		+	[[Category: Efremov, R G.]]
		+	[[Category: Sazanov, L A.]]
		+	[[Category: Complex i]]
		+	[[Category: Cytoplasmic membrane]]
		+	[[Category: Membrane protein]]
		+	[[Category: Nadh]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Proton pump]]
		+	[[Category: Ubiquinone]]

OCA at 06:31, 4 May 2011

OCA — Wed, 04 May 2011 06:31:56 GMT

←Older revision		Revision as of 06:31, 4 May 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rko is ON HOLD	+	The entry 3rko is ON HOLD until Paper Publication

	Authors: Efremov, R.G., Sazanov, L.A.		Authors: Efremov, R.G., Sazanov, L.A.

-	Description: Crystal structure of the membrane domain of respiratory complex I from E. coli	+	Description: Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution

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

OCA — Wed, 27 Apr 2011 06:58:01 GMT

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

←Older revision

Revision as of 06:58, 27 April 2011

OCA: New page: '''Unreleased structure''' The entry 3rko is ON HOLD Authors: Efremov, R.G., Sazanov, L.A. Description: Crystal structure of the membrane domain of respiratory complex I from E. coli

OCA — Wed, 27 Apr 2011 06:58:00 GMT

New page: '''Unreleased structure''' The entry 3rko is ON HOLD Authors: Efremov, R.G., Sazanov, L.A. Description: Crystal structure of the membrane domain of respiratory complex I from E. coli

New page

'''Unreleased structure'''

The entry 3rko is ON HOLD

Authors: Efremov, R.G., Sazanov, L.A.

Description: Crystal structure of the membrane domain of respiratory complex I from E. coli