3j46 - Revision history

OCA at 14:15, 24 January 2024

2024-01-24T14:15:23Z

←Older revision		Revision as of 14:15, 24 January 2024
Line 3:		Line 3:
	<SX load='3j46' size='340' side='right' viewer='molstar' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>		<SX load='3j46' size='340' side='right' viewer='molstar' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from ~~[https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and~~ [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j46]] is a 10 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=3J46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J46 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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]] 10.1Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2i2p\|2i2p]], [[3j01\|3j01]], [[3i8g\|3i8g]], [[3j45\|3j45]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [https://pdbe.org/3j46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [https://www.ebi.ac.uk/pdbsum/3j46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j46 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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [https://pdbe.org/3j46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [https://www.ebi.ac.uk/pdbsum/3j46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j46 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SECG_ECOLI SECG_ECOLI]] Subunit of the protein translocation channel SecYEG. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY. Treatment with antibiotics that block translation elongation such as chloramphenicol also leads to degradation of SecY and SecE but not SecG. [[https://www.uniprot.org/uniprot/RL1_ECOLI RL1_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318_B] [[https://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[https://www.uniprot.org/uniprot/SECE_ECOLI SECE_ECOLI]] Essential subunit of the protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY.<ref>PMID:15140892</ref> [[https://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[https://www.uniprot.org/uniprot/SECY_ECOLI SECY_ECOLI]] 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. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.[HAMAP-Rule:MF_01465] [[https://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374]	+	[https://www.uniprot.org/uniprot/SECY_ECOLI SECY_ECOLI] 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. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.[HAMAP-Rule:MF_01465]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Preprotein translocase\|Preprotein translocase]]	+	*[[Preprotein translocase 3D structures\|Preprotein translocase 3D structures]]
	*[[Ribosomal protein L23\|Ribosomal protein L23]]		*[[Ribosomal protein L23\|Ribosomal protein L23]]
	*[[Ribosomal protein L24\|Ribosomal protein L24]]		*[[Ribosomal protein L24\|Ribosomal protein L24]]
Line 30:		Line 30:
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Bacillus coli migula 1895]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Akey~~, C W~~]]	+	[[Category: Akey CW]]
-	[[Category: Gumbart~~, J C~~]]	+	[[Category: Gumbart JC]]
-	[[Category: Li, W]]	+	[[Category: Li W]]
-	[[Category: Ludtke~~, S J~~]]	+	[[Category: Ludtke SJ]]
-	[[Category: Menetret~~, J F~~]]	+	[[Category: Menetret JF]]
-	[[Category: Park, E]]	+	[[Category: Park E]]
-	[[Category: Rapoport~~, T A~~]]	+	[[Category: Rapoport TA]]
-	[[Category: Whynot, A]]	+	[[Category: Whynot A]]
-	~~[[Category: Nascent chain]]~~	+
-	~~[[Category: Preprotein translocase]]~~	+
-	~~[[Category: Protein translocation channel]]~~	+
-	~~[[Category: Ribosome-protein transport complex]]~~	+
-	~~[[Category: Secyeg~~]]	+

OCA at 03:49, 21 April 2022

2022-04-21T03:49:44Z

←Older revision		Revision as of 03:49, 21 April 2022
Line 3:		Line 3:
	<SX load='3j46' size='340' side='right' viewer='molstar' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>		<SX load='3j46' size='340' side='right' viewer='molstar' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [~~http~~://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3J46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J46 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i2p\|2i2p]], [[3j01\|3j01]], [[3i8g\|3i8g]], [[3j45\|3j45]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2i2p\|2i2p]], [[3j01\|3j01]], [[3i8g\|3i8g]], [[3j45\|3j45]]</div></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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [~~http~~://pdbe.org/3j46 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3j46 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3j46 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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [https://pdbe.org/3j46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [https://www.ebi.ac.uk/pdbsum/3j46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j46 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SECG_ECOLI SECG_ECOLI]] Subunit of the protein translocation channel SecYEG. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY. Treatment with antibiotics that block translation elongation such as chloramphenicol also leads to degradation of SecY and SecE but not SecG. [[~~http~~://www.uniprot.org/uniprot/RL1_ECOLI RL1_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318_B] [[~~http~~://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[~~http~~://www.uniprot.org/uniprot/SECE_ECOLI SECE_ECOLI]] Essential subunit of the protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY.<ref>PMID:15140892</ref> [[~~http~~://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[~~http~~://www.uniprot.org/uniprot/SECY_ECOLI SECY_ECOLI]] 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. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.[HAMAP-Rule:MF_01465] [[~~http~~://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374]	+	[[https://www.uniprot.org/uniprot/SECG_ECOLI SECG_ECOLI]] Subunit of the protein translocation channel SecYEG. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY. Treatment with antibiotics that block translation elongation such as chloramphenicol also leads to degradation of SecY and SecE but not SecG. [[https://www.uniprot.org/uniprot/RL1_ECOLI RL1_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318_B] [[https://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[https://www.uniprot.org/uniprot/SECE_ECOLI SECE_ECOLI]] Essential subunit of the protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY.<ref>PMID:15140892</ref> [[https://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[https://www.uniprot.org/uniprot/SECY_ECOLI SECY_ECOLI]] 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. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.[HAMAP-Rule:MF_01465] [[https://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 17:54, 10 April 2020

2020-04-10T17:54:31Z

←Older revision		Revision as of 17:54, 10 April 2020
Line 3:		Line 3:
	<SX load='3j46' size='340' side='right' viewer='molstar' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>		<SX load='3j46' size='340' side='right' viewer='molstar' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3J46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J46 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i2p\|2i2p]], [[3j01\|3j01]], [[3i8g\|3i8g]], [[3j45\|3j45]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i2p\|2i2p]], [[3j01\|3j01]], [[3i8g\|3i8g]], [[3j45\|3j45]]</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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [http://pdbe.org/3j46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [http://www.ebi.ac.uk/pdbsum/3j46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j46 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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [http://pdbe.org/3j46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [http://www.ebi.ac.uk/pdbsum/3j46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j46 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 17:22, 6 March 2020

2020-03-06T17:22:44Z

←Older revision		Revision as of 17:22, 6 March 2020
Line 1:		Line 1:

	==Structure of the SecY protein translocation channel in action==		==Structure of the SecY protein translocation channel in action==
-	<~~StructureSection~~ load='3j46' size='340' side='right'caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>	+	<SX load='3j46' size='340' side='right' viewer='molstar' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J46 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J46 FirstGlance]. <br>
Line 29:		Line 29:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 06:13, 3 July 2019

2019-07-03T06:13:22Z

←Older revision		Revision as of 06:13, 3 July 2019
Line 1:		Line 1:

	==Structure of the SecY protein translocation channel in action==		==Structure of the SecY protein translocation channel in action==
-	<StructureSection load='3j46' size='340' side='right' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>	+	<StructureSection load='3j46' size='340' side='right'caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J46 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J46 FirstGlance]. <br>
Line 25:		Line 25:
	*[[Ribosomal protein L24\|Ribosomal protein L24]]		*[[Ribosomal protein L24\|Ribosomal protein L24]]
	*[[Ribosomal protein L29\|Ribosomal protein L29]]		*[[Ribosomal protein L29\|Ribosomal protein L29]]
-	*[[~~TRNA~~\|~~TRNA~~]]	+	*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 32:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
	[[Category: Akey, C W]]		[[Category: Akey, C W]]
	[[Category: Gumbart, J C]]		[[Category: Gumbart, J C]]

OCA at 02:16, 5 August 2016

2016-08-05T02:16:39Z

←Older revision		Revision as of 02:16, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of the SecY protein translocation channel in action==		==Structure of the SecY protein translocation channel in action==
	<StructureSection load='3j46' size='340' side='right' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>		<StructureSection load='3j46' size='340' side='right' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i2p\|2i2p]], [[3j01\|3j01]], [[3i8g\|3i8g]], [[3j45\|3j45]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i2p\|2i2p]], [[3j01\|3j01]], [[3i8g\|3i8g]], [[3j45\|3j45]]</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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [http://www.ebi.ac.uk/pdbsum/3j46 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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [http://pdbe.org/3j46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [http://www.ebi.ac.uk/pdbsum/3j46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j46 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 3j46" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 23:		Line 25:
	*[[Ribosomal protein L24\|Ribosomal protein L24]]		*[[Ribosomal protein L24\|Ribosomal protein L24]]
	*[[Ribosomal protein L29\|Ribosomal protein L29]]		*[[Ribosomal protein L29\|Ribosomal protein L29]]
		+	*[[TRNA\|TRNA]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:01, 25 December 2014

2014-12-25T15:01:44Z

←Older revision		Revision as of 15:01, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3j46\| PDB=3j46 \| SCENE= }}~~	+	==Structure of the SecY protein translocation channel in action==
-	===Structure of the SecY protein translocation channel in action===	+	<StructureSection load='3j46' size='340' side='right' caption='[[3j46]], [[Resolution\|resolution]] 10.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24153188}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J46 FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i2p\|2i2p]], [[3j01\|3j01]], [[3i8g\|3i8g]], [[3j45\|3j45]]</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=3j46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j46 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j46 RCSB], [http://www.ebi.ac.uk/pdbsum/3j46 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/SECG_ECOLI SECG_ECOLI]] Subunit of the protein translocation channel SecYEG. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY. Treatment with antibiotics that block translation elongation such as chloramphenicol also leads to degradation of SecY and SecE but not SecG. [[http://www.uniprot.org/uniprot/RL1_ECOLI RL1_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318_B] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/SECE_ECOLI SECE_ECOLI]] Essential subunit of the protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY.<ref>PMID:15140892</ref> [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/SECY_ECOLI SECY_ECOLI]] 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. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.[HAMAP-Rule:MF_01465] [[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374]		[[http://www.uniprot.org/uniprot/SECG_ECOLI SECG_ECOLI]] Subunit of the protein translocation channel SecYEG. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY. Treatment with antibiotics that block translation elongation such as chloramphenicol also leads to degradation of SecY and SecE but not SecG. [[http://www.uniprot.org/uniprot/RL1_ECOLI RL1_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318_B] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/SECE_ECOLI SECE_ECOLI]] Essential subunit of the protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY.<ref>PMID:15140892</ref> [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/SECY_ECOLI SECY_ECOLI]] 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. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.[HAMAP-Rule:MF_01465] [[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis. Crystal structures of the inactive channel show that the SecY subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. The closed channel has an empty cytoplasmic funnel and an extracellular funnel that is filled with a small helical domain, called the plug. During initiation of translocation, a ribosome-nascent chain complex binds to the SecY (or Sec61) complex, resulting in insertion of the nascent chain. However, the mechanism of channel opening during translocation is unclear. Here we have addressed this question by determining structures of inactive and active ribosome-channel complexes with cryo-electron microscopy. Non-translating ribosome-SecY channel complexes derived from Methanocaldococcus jannaschii or Escherichia coli show the channel in its closed state, and indicate that ribosome binding per se causes only minor changes. The structure of an active E. coli ribosome-channel complex demonstrates that the nascent chain opens the channel, causing mostly rigid body movements of the amino- and carboxy-terminal halves of SecY. In this early translocation intermediate, the polypeptide inserts as a loop into the SecY channel with the hydrophobic signal sequence intercalated into the open lateral gate. The nascent chain also forms a loop on the cytoplasmic surface of SecY rather than entering the channel directly.

-	~~==About this~~ Structure==	+	Structure of the SecY channel during initiation of protein translocation.,Park E, Menetret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW Nature. 2013 Oct 23. doi: 10.1038/nature12720. PMID:24153188<ref>PMID:24153188</ref>
-	~~[[3j46]] is a 14 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http~~:~~//en~~.~~wikipedia.org/wiki~~/~~Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3J46 OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
		+	*[[Preprotein translocase\|Preprotein translocase]]
	*[[Ribosomal protein L23\|Ribosomal protein L23]]		*[[Ribosomal protein L23\|Ribosomal protein L23]]
	*[[Ribosomal protein L24\|Ribosomal protein L24]]		*[[Ribosomal protein L24\|Ribosomal protein L24]]
	*[[Ribosomal protein L29\|Ribosomal protein L29]]		*[[Ribosomal protein L29\|Ribosomal protein L29]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024153188</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Akey, C W.]]	+	[[Category: Akey, C W]]
-	[[Category: Gumbart, J C.]]	+	[[Category: Gumbart, J C]]
-	[[Category: Li, W.]]	+	[[Category: Li, W]]
-	[[Category: Ludtke, S J.]]	+	[[Category: Ludtke, S J]]
-	[[Category: Menetret, J F.]]	+	[[Category: Menetret, J F]]
-	[[Category: Park, E.]]	+	[[Category: Park, E]]
-	[[Category: Rapoport, T A.]]	+	[[Category: Rapoport, T A]]
-	[[Category: Whynot, A~~.]]~~	+	[[Category: Whynot, A]]
-	~~[[Category: 70~~]]	+
	[[Category: Nascent chain]]		[[Category: Nascent chain]]
	[[Category: Preprotein translocase]]		[[Category: Preprotein translocase]]

OCA at 08:57, 5 February 2014

2014-02-05T08:57:31Z

←Older revision		Revision as of 08:57, 5 February 2014
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Cortinarius_roseobulbus Cortinarius roseobulbus~~], [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli~~] and [http://en.wikipedia.org/wiki/Gekko_coi Gekko coi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA].	+	[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA].
		+
		+	==See Also==
		+	*[[Ribosomal protein L23\|Ribosomal protein L23]]
		+	*[[Ribosomal protein L24\|Ribosomal protein L24]]
		+	*[[Ribosomal protein L29\|Ribosomal protein L29]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:024153188</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024153188</ref><references group="xtra"/><references/>
-	[[Category: ~~Cortinarius roseobulbus~~]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Gekko coi]]
	[[Category: Akey, C W.]]		[[Category: Akey, C W.]]
	[[Category: Gumbart, J C.]]		[[Category: Gumbart, J C.]]

OCA at 05:42, 6 November 2013

2013-11-06T05:42:59Z

←Older revision		Revision as of 05:42, 6 November 2013
Line 1:		Line 1:
	{{STRUCTURE_3j46\| PDB=3j46 \| SCENE= }}		{{STRUCTURE_3j46\| PDB=3j46 \| SCENE= }}
	===Structure of the SecY protein translocation channel in action===		===Structure of the SecY protein translocation channel in action===
		+	{{ABSTRACT_PUBMED_24153188}}

	==Function==		==Function==
Line 9:		Line 10:

	==Reference==		==Reference==
-	<references group="xtra"/><references/>	+	<ref group="xtra">PMID:024153188</ref><references group="xtra"/><references/>
	[[Category: Cortinarius roseobulbus]]		[[Category: Cortinarius roseobulbus]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 06:49, 23 October 2013

2013-10-23T06:49:40Z

←Older revision		Revision as of 06:49, 23 October 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3j46\| PDB=3j46 \| SCENE= }}
		+	===Structure of the SecY protein translocation channel in action===

-	The ~~entry 3j46~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/SECG_ECOLI SECG_ECOLI]] Subunit of the protein translocation channel SecYEG. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY. Treatment with antibiotics that block translation elongation such as chloramphenicol also leads to degradation of SecY and SecE but not SecG. [[http://www.uniprot.org/uniprot/RL1_ECOLI RL1_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318_B] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/SECE_ECOLI SECE_ECOLI]] Essential subunit of the protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true it also results in FtsH-mediated degradation of SecY.<ref>PMID:15140892</ref> [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/SECY_ECOLI SECY_ECOLI]] 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. SecY is required to insert newly synthesized SecY into the inner membrane. Overexpression of some hybrid proteins has been thought to jam the protein secretion apparatus resulting in cell death; while this may be true, overexpression also results in FtsH-mediated degradation of SecY.[HAMAP-Rule:MF_01465] [[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374]

-	~~Authors~~: ~~Akey, C~~.W., ~~Park, E~~.~~, Menetret, J~~.F.~~, Gumbart, J~~.C.~~, Ludtke, S~~.J.~~, Li, W., Whynot, A., Rapoport, T~~.A.	+	==About this Structure==
		+	[[3j46]] is a 14 chain structure with sequence from [http://en.wikipedia.org/wiki/Cortinarius_roseobulbus Cortinarius roseobulbus], [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Gekko_coi Gekko coi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J46 OCA].

-	~~Description~~: ~~Structure of the SecY protein~~ translocation channel ~~in action~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Cortinarius roseobulbus]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Gekko coi]]
		+	[[Category: Akey, C W.]]
		+	[[Category: Gumbart, J C.]]
		+	[[Category: Li, W.]]
		+	[[Category: Ludtke, S J.]]
		+	[[Category: Menetret, J F.]]
		+	[[Category: Park, E.]]
		+	[[Category: Rapoport, T A.]]
		+	[[Category: Whynot, A.]]
		+	[[Category: 70]]
		+	[[Category: Nascent chain]]
		+	[[Category: Preprotein translocase]]
		+	[[Category: Protein translocation channel]]
		+	[[Category: Ribosome-protein transport complex]]
		+	[[Category: Secyeg]]