3ias - Revision history

OCA at 07:42, 6 September 2023

OCA — Wed, 06 Sep 2023 07:42:01 GMT

←Older revision		Revision as of 07:42, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3ias' size='340' side='right'caption='[[3ias]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='3ias' size='340' side='right'caption='[[3ias]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ias]] is a 32 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thermus_thermophilus~~ Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3IAS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ias]] is a 32 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IAS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 3.15Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fug\|2fug]], [[3i9v\|3i9v]], [[3iam\|3iam]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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_(quinone) NADH dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.11 1.6.5.11] </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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [https://pdbe.org/3ias PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [https://www.ebi.ac.uk/pdbsum/3ias PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ias ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [~~http~~://pdbe.org/3ias PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ias PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ias ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/NQO6_THET8 NQO6_THET8]] 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 menaquinone. 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 required for the synthesis of ATP.[HAMAP-Rule:MF_01356] [[http://www.uniprot.org/uniprot/NQO3_THET8 NQO3_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO9_THET8 NQO9_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits.[HAMAP-Rule:MF_01351] [[http://www.uniprot.org/uniprot/NQO2_THET8 NQO2_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO15_THET8 NQO15_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo15 subunit has probably a role in complex stabilization, and may be also involved in the storage of iron for iron-sulfur cluster regeneration in the complex.<ref>PMID:16469879</ref> [[http://www.uniprot.org/uniprot/NQO1_THET8 NQO1_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. [[http://www.uniprot.org/uniprot/NQO4_THET8 NQO4_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo4 subunit may contain the quinone-binding site.[HAMAP-Rule:MF_01358] [[http://www.uniprot.org/uniprot/NQO5_THET8 NQO5_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo5 subunit may be involved in the stabilization of the complex.[HAMAP-Rule:MF_01357]	+	[https://www.uniprot.org/uniprot/NQO1_THET8 NQO1_THET8] 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 menaquinone. 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 required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Thermus thermophilus]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Berrisford~~, J M~~]]	+	[[Category: Berrisford JM]]
-	[[Category: Sazanov~~, L A]]~~	+	[[Category: Sazanov LA]]
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Respiratory chain~~]]	+

OCA at 11:54, 23 September 2020

OCA — Wed, 23 Sep 2020 11:54:09 GMT

←Older revision		Revision as of 11:54, 23 September 2020
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution==		==Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution==
-	<StructureSection load='3ias' size='340' side='right' caption='[[3ias]], [[Resolution\|resolution]] 3.15Å' scene=''>	+	<StructureSection load='3ias' size='340' side='right'caption='[[3ias]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ias]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IAS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ias]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3IAS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fug\|2fug]], [[3i9v\|3i9v]], [[3iam\|3iam]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fug\|2fug]], [[3i9v\|3i9v]], [[3iam\|3iam]]</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_(quinone) NADH dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.11 1.6.5.11] </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_dehydrogenase_(quinone) NADH dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.11 1.6.5.11] </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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://pdbe.org/3ias PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ias ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://pdbe.org/3ias PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ias ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/NQO6_THET8 NQO6_THET8]] 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 menaquinone. 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 required for the synthesis of ATP.[HAMAP-Rule:MF_01356] [[http://www.uniprot.org/uniprot/NQO3_THET8 NQO3_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO9_THET8 NQO9_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits.[HAMAP-Rule:MF_01351] [[http://www.uniprot.org/uniprot/NQO2_THET8 NQO2_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO15_THET8 NQO15_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo15 subunit has probably a role in complex stabilization, and may be also involved in the storage of iron for iron-sulfur cluster regeneration in the complex.<ref>PMID:16469879</ref> [[http://www.uniprot.org/uniprot/NQO1_THET8 NQO1_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. [[http://www.uniprot.org/uniprot/NQO4_THET8 NQO4_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo4 subunit may contain the quinone-binding site.[HAMAP-Rule:MF_01358] [[http://www.uniprot.org/uniprot/NQO5_THET8 NQO5_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo5 subunit may be involved in the stabilization of the complex.[HAMAP-Rule:MF_01357]		[[http://www.uniprot.org/uniprot/NQO6_THET8 NQO6_THET8]] 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 menaquinone. 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 required for the synthesis of ATP.[HAMAP-Rule:MF_01356] [[http://www.uniprot.org/uniprot/NQO3_THET8 NQO3_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO9_THET8 NQO9_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits.[HAMAP-Rule:MF_01351] [[http://www.uniprot.org/uniprot/NQO2_THET8 NQO2_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO15_THET8 NQO15_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo15 subunit has probably a role in complex stabilization, and may be also involved in the storage of iron for iron-sulfur cluster regeneration in the complex.<ref>PMID:16469879</ref> [[http://www.uniprot.org/uniprot/NQO1_THET8 NQO1_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. [[http://www.uniprot.org/uniprot/NQO4_THET8 NQO4_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo4 subunit may contain the quinone-binding site.[HAMAP-Rule:MF_01358] [[http://www.uniprot.org/uniprot/NQO5_THET8 NQO5_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo5 subunit may be involved in the stabilization of the complex.[HAMAP-Rule:MF_01357]
Line 38:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Berrisford, J M]]		[[Category: Berrisford, J M]]

OCA at 09:27, 19 December 2018

OCA — Wed, 19 Dec 2018 09:27:12 GMT

←Older revision		Revision as of 09:27, 19 December 2018
Line 1:		Line 1:
		+	{{Large structure}}
	==Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution==		==Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution==
	<StructureSection load='3ias' size='340' side='right' caption='[[3ias]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='3ias' size='340' side='right' caption='[[3ias]], [[Resolution\|resolution]] 3.15Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fug\|2fug]], [[3i9v\|3i9v]], [[3iam\|3iam]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fug\|2fug]], [[3i9v\|3i9v]], [[3iam\|3iam]]</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_(quinone) NADH dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.11 1.6.5.11] </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_dehydrogenase_(quinone) NADH dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.11 1.6.5.11] </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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://pdbe.org/3ias PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias 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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://pdbe.org/3ias PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ias ProSAT]</span></td></tr>
	</table>		</table>
	{{Large structure}}		{{Large structure}}
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ia/3ias_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ia/3ias_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>

OCA at 00:40, 9 February 2016

OCA — Tue, 09 Feb 2016 00:40:32 GMT

←Older revision		Revision as of 00:40, 9 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fug\|2fug]], [[3i9v\|3i9v]], [[3iam\|3iam]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fug\|2fug]], [[3i9v\|3i9v]], [[3iam\|3iam]]</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_(quinone) NADH dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6~~.99~~.5 1.6~~.99~~.5] </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_dehydrogenase_(quinone) NADH dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.5.11 1.6.5.11] </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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias 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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://pdbe.org/3ias PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias PDBsum]</span></td></tr>
	</table>		</table>
		+	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/NQO6_THET8 NQO6_THET8]] 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 menaquinone. 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 required for the synthesis of ATP.[HAMAP-Rule:MF_01356] [[http://www.uniprot.org/uniprot/NQO3_THET8 NQO3_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO9_THET8 NQO9_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits.[HAMAP-Rule:MF_01351] [[http://www.uniprot.org/uniprot/NQO2_THET8 NQO2_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO15_THET8 NQO15_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo15 subunit has probably a role in complex stabilization, and may be also involved in the storage of iron for iron-sulfur cluster regeneration in the complex.<ref>PMID:16469879</ref> [[http://www.uniprot.org/uniprot/NQO1_THET8 NQO1_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. [[http://www.uniprot.org/uniprot/NQO4_THET8 NQO4_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo4 subunit may contain the quinone-binding site.[HAMAP-Rule:MF_01358] [[http://www.uniprot.org/uniprot/NQO5_THET8 NQO5_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo5 subunit may be involved in the stabilization of the complex.[HAMAP-Rule:MF_01357]		[[http://www.uniprot.org/uniprot/NQO6_THET8 NQO6_THET8]] 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 menaquinone. 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 required for the synthesis of ATP.[HAMAP-Rule:MF_01356] [[http://www.uniprot.org/uniprot/NQO3_THET8 NQO3_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO9_THET8 NQO9_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits.[HAMAP-Rule:MF_01351] [[http://www.uniprot.org/uniprot/NQO2_THET8 NQO2_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO15_THET8 NQO15_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo15 subunit has probably a role in complex stabilization, and may be also involved in the storage of iron for iron-sulfur cluster regeneration in the complex.<ref>PMID:16469879</ref> [[http://www.uniprot.org/uniprot/NQO1_THET8 NQO1_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. [[http://www.uniprot.org/uniprot/NQO4_THET8 NQO4_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo4 subunit may contain the quinone-binding site.[HAMAP-Rule:MF_01358] [[http://www.uniprot.org/uniprot/NQO5_THET8 NQO5_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo5 subunit may be involved in the stabilization of the complex.[HAMAP-Rule:MF_01357]
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=3ias 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 3ias" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[NADH-quinone oxidoreductase\|NADH-quinone oxidoreductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:16, 25 December 2014

OCA — Thu, 25 Dec 2014 03:16:02 GMT

←Older revision		Revision as of 03:16, 25 December 2014
Line 8:		Line 8:
	<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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias 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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NQO6_THET8 NQO6_THET8]] 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 menaquinone. 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 required for the synthesis of ATP.[HAMAP-Rule:MF_01356] [[http://www.uniprot.org/uniprot/NQO3_THET8 NQO3_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO9_THET8 NQO9_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits.[HAMAP-Rule:MF_01351] [[http://www.uniprot.org/uniprot/NQO2_THET8 NQO2_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO15_THET8 NQO15_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo15 subunit has probably a role in complex stabilization, and may be also involved in the storage of iron for iron-sulfur cluster regeneration in the complex.<ref>PMID:16469879</ref> [[http://www.uniprot.org/uniprot/NQO1_THET8 NQO1_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. [[http://www.uniprot.org/uniprot/NQO4_THET8 NQO4_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo4 subunit may contain the quinone-binding site.[HAMAP-Rule:MF_01358] [[http://www.uniprot.org/uniprot/NQO5_THET8 NQO5_THET8]] 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 menaquinone. 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 required for the synthesis of ATP. The nqo5 subunit may be involved in the stabilization of the complex.[HAMAP-Rule:MF_01357]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:19, 18 December 2014

OCA — Thu, 18 Dec 2014 06:19:47 GMT

←Older revision		Revision as of 06:19, 18 December 2014
Line 1:		Line 1:
-	~~{{Large structure}}~~	+	==Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution==
-	~~{{STRUCTURE_3ias\| PDB=3ias \| SCENE= }}~~	+	<StructureSection load='3ias' size='340' side='right' caption='[[3ias]], [[Resolution\|resolution]] 3.15Å' scene=''>
-	===Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution===	+	== Structural highlights ==
-	~~{{ABSTRACT_PUBMED_19635800}}~~	+	<table><tr><td colspan='2'>[[3ias]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IAS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fug\|2fug]], [[3i9v\|3i9v]], [[3iam\|3iam]]</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_(quinone) NADH dehydrogenase (quinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.99.5 1.6.99.5] </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=3ias FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ias OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ias RCSB], [http://www.ebi.ac.uk/pdbsum/3ias 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/ia/3ias_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 ==
		+	Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 A resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several alpha-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.

-	~~==About this Structure==~~	+	Structural basis for the mechanism of respiratory complex I.,Berrisford JM, Sazanov LA J Biol Chem. 2009 Oct 23;284(43):29773-83. Epub 2009 Jul 27. PMID:19635800<ref>PMID:19635800</ref>
-	~~[[3ias]] is a 32 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3IAS OCA].~~	+

-	~~==Reference==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<~~ref group="xtra"~~>~~PMID:019635800~~</~~ref~~>~~<ref group~~=~~"xtra">PMID:016469879~~</~~ref~~><~~references group="xtra"~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Berrisford, J M.]]	+	[[Category: Berrisford, J M]]
-	[[Category: Sazanov, L A.]]	+	[[Category: Sazanov, L A]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Respiratory chain]]		[[Category: Respiratory chain]]

OCA at 07:48, 11 March 2013

OCA — Mon, 11 Mar 2013 07:48:42 GMT

←Older revision		Revision as of 07:48, 11 March 2013
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-	~~[[Image:3ias.png\|left\|200px]]~~	+	{{Large structure}}
-		+
-	~~<!--~~	+
-	~~The line below this paragraph, containing "STRUCTURE_3ias", 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),~~	+
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-	~~-->~~	+
	{{STRUCTURE_3ias\| PDB=3ias \| SCENE= }}		{{STRUCTURE_3ias\| PDB=3ias \| SCENE= }}
-
	===Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution===		===Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, oxidized, 4 mol/ASU, re-refined to 3.15 angstrom resolution===
-
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-	<!--
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	{{ABSTRACT_PUBMED_19635800}}		{{ABSTRACT_PUBMED_19635800}}

	==About this Structure==		==About this Structure==
-	[[3ias]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus_hb8~~ Thermus thermophilus ~~hb8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA].	+	[[3ias]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19635800~~</ref><ref group="xtra">PMID:~~16469879~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019635800</ref><ref group="xtra">PMID:016469879</ref><references group="xtra"/>
-	[[Category: Thermus thermophilus ~~hb8~~]]	+	[[Category: Thermus thermophilus]]
	[[Category: Berrisford, J M.]]		[[Category: Berrisford, J M.]]
	[[Category: Sazanov, L A.]]		[[Category: Sazanov, L A.]]

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

OCA — Mon, 14 Mar 2011 19:51:37 GMT

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

←Older revision

Revision as of 19:51, 14 March 2011

OCA at 19:51, 14 March 2011

OCA — Mon, 14 Mar 2011 19:51:36 GMT

←Older revision		Revision as of 19:51, 14 March 2011
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-	{{Seed}}
	[[Image:3ias.png\|left\|200px]]		[[Image:3ias.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3IAS~~ is a 32 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA].	+	[[3ias]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IAS OCA].

	==Reference==		==Reference==
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	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Respiratory chain]]		[[Category: Respiratory chain]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 4 12:38:11 2009''

OCA at 10:38, 4 November 2009

OCA — Wed, 04 Nov 2009 10:38:16 GMT

←Older revision		Revision as of 10:38, 4 November 2009
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-	[[Image:3ias.~~jpg~~\|left\|200px]]	+	[[Image:3ias.png\|left\|200px]]

	<!--		<!--
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	[[Category: Respiratory chain]]		[[Category: Respiratory chain]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 16 09~~:02:11 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 4 12:38:11 2009''