5t4p: Difference between revisions

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 ==Autoinhibited E. coli ATP synthase state 2==
-<StructureSection load='5t4p' size='340' side='right' caption='[[5t4p]], [[Resolution|resolution]] 7.77&Aring;' scene=''>
+<SX load='5t4p' size='340' side='right' viewer='molstar' caption='[[5t4p]], [[Resolution|resolution]] 7.77&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5t4p]] is a 22 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=5T4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T4P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5t4p]] is a 22 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=5T4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T4P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 7.77&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5t4o|5t4o]], [[5t4q|5t4q]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">atpA, ECS88_4156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), atpD, ECS88_4154 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), atpG, ECS88_4155 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), atpC, ECS88_4153 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), atpF, Z5234, ECs4678 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), atpB, EC55989_4213 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), atpH, ECS88_4157 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), atpE, ECIAI39_4341 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4p OCA], [https://pdbe.org/5t4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t4p RCSB], [https://www.ebi.ac.uk/pdbsum/5t4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4p ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/H(+)-transporting_two-sector_ATPase H(+)-transporting two-sector ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.14 3.6.3.14] </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=5t4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4p OCA], [http://pdbe.org/5t4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t4p RCSB], [http://www.ebi.ac.uk/pdbsum/5t4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4p ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ATP6_ECO55 ATP6_ECO55]] Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. [[http://www.uniprot.org/uniprot/ATPG_ECO45 ATPG_ECO45]] Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. [[http://www.uniprot.org/uniprot/ATPD_ECO45 ATPD_ECO45]] F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation.  This protein is part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) to CF(1) or is implicated in proton conduction. [[http://www.uniprot.org/uniprot/ATPB_ECO45 ATPB_ECO45]] Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. [[http://www.uniprot.org/uniprot/ATPL_ECO7I ATPL_ECO7I]] F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation.  Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of between 10-14 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits. [[http://www.uniprot.org/uniprot/ATPA_ECO45 ATPA_ECO45]] Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit. [[http://www.uniprot.org/uniprot/ATPE_ECO45 ATPE_ECO45]] Produces ATP from ADP in the presence of a proton gradient across the membrane. [[http://www.uniprot.org/uniprot/ATPF_ECO57 ATPF_ECO57]] F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation.  Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0).
+[https://www.uniprot.org/uniprot/ATPA_ECOLI ATPA_ECOLI] Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit.[HAMAP-Rule:MF_01346]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-A molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk's epsilon subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30 degrees to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates towards the membrane with its helices separating to embrace subunit a from two sides.
-Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states.,Sobti M, Smits C, Wong AS, Ishmukhametov R, Stock D, Sandin S, Stewart AG Elife. 2016 Dec 21;5. pii: e21598. doi: 10.7554/eLife.21598. PMID:28001127<ref>PMID:28001127</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5t4p" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[ATPase|ATPase]]
+*[[ATPase 3D structures|ATPase 3D structures]]
-== References ==
-<references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Ishmukhametov, R]]
+[[Category: Large Structures]]
-[[Category: Sandin, S]]
+[[Category: Ishmukhametov R]]
-[[Category: Smits, C]]
+[[Category: Sandin S]]
-[[Category: Sobti, M]]
+[[Category: Smits C]]
-[[Category: Stewart, A G]]
+[[Category: Sobti M]]
-[[Category: Stock, D]]
+[[Category: Stewart AG]]
-[[Category: Wong, A S.W]]
+[[Category: Stock D]]
-[[Category: Atp synthase]]
+[[Category: Wong ASW]]
-[[Category: Atpase]]
-[[Category: Hydrolase]]
-[[Category: Membrane protein]]
-[[Category: Rotary motor]]