6itc: Difference between revisions

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 ==Structure of a substrate engaged SecA-SecY protein translocation machine==
-<StructureSection load='6itc' size='340' side='right'caption='[[6itc]], [[Resolution|resolution]] 3.45&Aring;' scene=''>
+<SX load='6itc' size='340' side='right' viewer='molstar' caption='[[6itc]], [[Resolution|resolution]] 3.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6itc]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ITC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ITC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6itc]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria], [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168], [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ITC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ITC 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=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGV:(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+(11E)-OCTADEC-11-ENOATE'>PGV</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]] 3.45&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene></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=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=GYS:[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGV:(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+(11E)-OCTADEC-11-ENOATE'>PGV</scene></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=6itc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6itc OCA], [http://pdbe.org/6itc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6itc RCSB], [http://www.ebi.ac.uk/pdbsum/6itc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6itc 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=6itc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6itc OCA], [https://pdbe.org/6itc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6itc RCSB], [https://www.ebi.ac.uk/pdbsum/6itc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6itc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin. [[http://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU]] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] [[http://www.uniprot.org/uniprot/A4IJK8_GEOTN A4IJK8_GEOTN]] The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently.[HAMAP-Rule:MF_01465][RuleBase:RU000537]
+[https://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are transported post-translationally through the SecY channel by the SecA ATPase. How a polypeptide is moved through the SecA-SecY complex is poorly understood, as structural information is lacking. Here, we report an electron cryo-microscopy (cryo-EM) structure of a translocating SecA-SecY complex in a lipid environment. The translocating polypeptide chain can be traced through both SecA and SecY. In the captured transition state of ATP hydrolysis, SecA's two-helix finger is close to the polypeptide, while SecA's clamp interacts with the polypeptide in a sequence-independent manner by inducing a short beta-strand. Taking into account previous biochemical and biophysical data, our structure is consistent with a model in which the two-helix finger and clamp cooperate during the ATPase cycle to move a polypeptide through the channel.
+Structure of the substrate-engaged SecA-SecY protein translocation machine.,Ma C, Wu X, Sun D, Park E, Catipovic MA, Rapoport TA, Gao N, Li L Nat Commun. 2019 Jun 28;10(1):2872. doi: 10.1038/s41467-019-10918-2. PMID:31253804<ref>PMID:31253804</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6itc" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
+*[[Preprotein translocase 3D structures|Preprotein translocase 3D structures]]
+*[[SecA|SecA]]
+== References ==
+<references/>
 __TOC__
-</StructureSection>
+</SX>
+[[Category: Aequorea victoria]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
+[[Category: Escherichia coli]]
+[[Category: Geobacillus thermodenitrificans NG80-2]]
+[[Category: Lama glama]]
 [[Category: Large Structures]]
-[[Category: Gao, N]]
+[[Category: Gao N]]
-[[Category: Long, L]]
+[[Category: Long L]]
-[[Category: Ma, C Y]]
+[[Category: Ma CY]]
-[[Category: Park, E Y]]
+[[Category: Park EY]]
-[[Category: Rapoport, T A]]
+[[Category: Rapoport TA]]
-[[Category: Sun, D J]]
+[[Category: Sun DJ]]
-[[Category: Wu, X F]]
+[[Category: Wu XF]]
-[[Category: Cryo-em]]
-[[Category: Protein transport]]
-[[Category: Seca]]
-[[Category: Secy]]
-[[Category: Translocation]]