5i4r - Revision history

OCA at 08:23, 23 August 2023

OCA — Wed, 23 Aug 2023 08:23:11 GMT

←Older revision		Revision as of 08:23, 23 August 2023
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	<StructureSection load='5i4r' size='340' side='right'caption='[[5i4r]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='5i4r' size='340' side='right'caption='[[5i4r]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i4r]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Econc Econc~~] 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=5I4R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I4R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i4r]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)] and [https://en.wikipedia.org/wiki/Escherichia_coli_NC101 Escherichia coli NC101]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I4R FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=GDP:GUANOSINE~~-~~5-DIPHOSPHATE'>GDP</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]] 3.3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5i4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i4r OCA], [~~http~~://pdbe.org/5i4r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i4r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i4r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i4r 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=5i4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i4r OCA], [https://pdbe.org/5i4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i4r RCSB], [https://www.ebi.ac.uk/pdbsum/5i4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i4r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~EFTU1_ECO24 EFTU1_ECO24~~]~~] This~~ protein ~~promotes~~ the ~~GTP~~-dependent ~~binding~~ of ~~aminoacyl~~-tRNA to the A-site of ~~ribosomes during~~ protein ~~biosynthesis~~.~~[HAMAP~~-~~Rule~~:~~MF_00118]~~	+	[https://www.uniprot.org/uniprot/CDIA_ECONC CDIA_ECONC] Toxic component of a toxin-immunity protein module, which functions as a cellular contact-dependent growth inhibition (CDI) system. CDI modules allow bacteria to communicate with and inhibit the growth of closely related neighboring bacteria in a contact-dependent fashion (target cell counts decrease about 10,0000-fold for this system). CdiA toxicity is neutralized by its cognate immunity protein CdiI-NC101, but not by CdiI from other bacteria (PubMed:26305955, PubMed:28973472). The C-terminal domain (CT) cleaves tRNA endonucleolytically at the 5' side of guanine discriminator nucleotide sites (removes the last 4 nucleotides of the tRNA acceptor arm when the first nucleotide to be removed is G) (PubMed:28973472). Requires EF-Ts (tsf) for toxic function of the CT domain in vivo (PubMed:28223500). In vitro the CT tRNase activity requires both EF-Tu (tufA) and EF-Ts. EF-Ts probably increases steady-state GTP-EF-Tu-aa-tRNA substrate levels. The CT domain is thought to remodel this same complex to displace the 3'-end of the aa-tRNA and allow it to enter into the toxin active site (PubMed:28973472). The CT domain gains access to the cytoplasm of target cells by using integral inner membrane protein PTS system glucose-specific EIICB component (ptsG) (PubMed:26305955).<ref>PMID:26305955</ref> <ref>PMID:28223500</ref> <ref>PMID:28973472</ref> The CdiA protein is thought to be exported from the cell through the central lumen of CdiB, the other half of its two-partner system (TPS). The TPS domain probably remains associated with CdiB while the FHA-1 domain forms an extended filament with the receptor-binding domain (RBD) at its extremity; in the secretion arrested state the C-terminus of the RBD and YP domains form a hairpin-like structure as the FHA-2, PT and CT domains are periplasmic. The YP domain is probably responsible for this arrest at the point where it re-enters the host cell periplasm. Upon binding to a target cell outer membrane receptor a signal is transmitted to activate secretion. The filament elongates slightly, the rest of CdiA is secreted and the FHA-2 domain becomes stably associated with the target cell's outer membrane where it facilitates entry of the toxic CT domain into the target cell periplasm. From there the toxic CT domain is cleaved and gains access to the target cell cytoplasm via an inner membrane protein (PtsG for this CDI).<ref>PMID:26305955</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Econc]]~~	+	[[Category: Escherichia coli NC101]]
-	[[Category: Escherichia coli]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Eschenfeldt, W]]	+	[[Category: Eschenfeldt W]]
-	[[Category: Goulding~~, C W~~]]	+	[[Category: Goulding CW]]
-	[[Category: Hayes~~, C S~~]]	+	[[Category: Hayes CS]]
-	[[Category: Joachimiak, A]]	+	[[Category: Joachimiak A]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Michalska K]]
-	[[Category: Michalska, K]]	+	[[Category: Stols L]]
-	[[Category: Stols, L]]	+
-	~~[[Category: UC4CDI, Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes]]~~	+
-	~~[[Category: Antitoxin]]~~	+
-	~~[[Category: Elongation factor]]~~	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Structure-function analysis of polymorphic cdi toxin-immunity protein complex]]~~	+
-	~~[[Category: Toxin]]~~	+
-	~~[[Category: Toxin-antitoxin complex]]~~	+
-	~~[[Category: Uc4cdi~~]]	+

OCA at 11:45, 25 December 2019

OCA — Wed, 25 Dec 2019 11:45:36 GMT

←Older revision		Revision as of 11:45, 25 December 2019
Line 1:		Line 1:

	==Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)==		==Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)==
-	<StructureSection load='5i4r' size='340' side='right' caption='[[5i4r]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='5i4r' size='340' side='right'caption='[[5i4r]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i4r]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] 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=5I4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I4R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i4r]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Econc Econc] 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=5I4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I4R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5i4r" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i4r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Econc]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
	[[Category: Eschenfeldt, W]]		[[Category: Eschenfeldt, W]]
	[[Category: Goulding, C W]]		[[Category: Goulding, C W]]

OCA at 07:00, 25 October 2017

OCA — Wed, 25 Oct 2017 07:00:54 GMT

←Older revision		Revision as of 07:00, 25 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i4r is ~~ON HOLD until Paper~~ Publication	+	==Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)==
		+	<StructureSection load='5i4r' size='340' side='right' caption='[[5i4r]], [[Resolution\|resolution]] 3.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5i4r]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] 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=5I4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I4R FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=5i4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i4r OCA], [http://pdbe.org/5i4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i4r RCSB], [http://www.ebi.ac.uk/pdbsum/5i4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i4r ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/EFTU1_ECO24 EFTU1_ECO24]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP.EF-Tu.aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP.EF-Tu.aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a beta-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Together, these observations suggest that the toxin remodels GTP.EF-Tu.aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.

-	~~Authors:~~ Michalska, K., Stols~~, L.~~, Eschenfeldt, W., ~~Hayes, C.S.~~, Goulding~~, C.W.~~, Joachimiak, A.~~, Midwest Center for Structural Genomics~~ (~~MCSG~~)~~, Structure~~-~~Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)~~	+	Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs.,Michalska K, Gucinski GC, Garza-Sanchez F, Johnson PM, Stols LM, Eschenfeldt WH, Babnigg G, Low DA, Goulding CW, Joachimiak A, Hayes CS Nucleic Acids Res. 2017 Sep 29;45(17):10306-10320. doi: 10.1093/nar/gkx700. PMID:28973472<ref>PMID:28973472</ref>

-	~~Description: Contact-dependent inhibition system from Escherichia coli NC101 -ternary CdiA~~/~~CdiI~~/EF-~~Tu complex (trypsin~~-~~modified)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5i4r" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Eschenfeldt, W]]
		+	[[Category: Goulding, C W]]
		+	[[Category: Hayes, C S]]
		+	[[Category: Joachimiak, A]]
		+	[[Category: Structural genomic]]
	[[Category: Michalska, K]]		[[Category: Michalska, K]]
	[[Category: Stols, L]]		[[Category: Stols, L]]
-	[[Category: ~~Hayes~~, ~~C.S~~]]	+	[[Category: UC4CDI, Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes]]
-	[[Category: ~~Joachimiak, A~~]]	+	[[Category: Antitoxin]]
-	[[Category: ~~Goulding, C.W~~]]	+	[[Category: Elongation factor]]
-	[[Category: ~~Midwest Center For Structural Genomics (~~Mcsg), Structure-~~Function Analysis Of Polymorphic Cdi~~ Toxin-~~Immunity Protein Complexes (Uc4cdi)~~]]	+	[[Category: Mcsg]]
-	[[Category: ~~Eschenfeldt, W~~]]	+	[[Category: Psi-biology]]
		+	[[Category: Structure-function analysis of polymorphic cdi toxin-immunity protein complex]]
		+	[[Category: Toxin]]
		+	[[Category: Toxin-antitoxin complex]]
		+	[[Category: Uc4cdi]]

OCA at 09:32, 9 March 2017

OCA — Thu, 09 Mar 2017 09:32:47 GMT

←Older revision		Revision as of 09:32, 9 March 2017
Line 9:		Line 9:
	[[Category: Michalska, K]]		[[Category: Michalska, K]]
	[[Category: Stols, L]]		[[Category: Stols, L]]
-	[[Category: Joachimiak, A]]
	[[Category: Hayes, C.S]]		[[Category: Hayes, C.S]]
		+	[[Category: Joachimiak, A]]
	[[Category: Goulding, C.W]]		[[Category: Goulding, C.W]]
	[[Category: Midwest Center For Structural Genomics (Mcsg), Structure-Function Analysis Of Polymorphic Cdi Toxin-Immunity Protein Complexes (Uc4cdi)]]		[[Category: Midwest Center For Structural Genomics (Mcsg), Structure-Function Analysis Of Polymorphic Cdi Toxin-Immunity Protein Complexes (Uc4cdi)]]
	[[Category: Eschenfeldt, W]]		[[Category: Eschenfeldt, W]]

OCA at 00:12, 11 May 2016

OCA — Wed, 11 May 2016 00:12:25 GMT

←Older revision		Revision as of 00:12, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5i4r is ON HOLD	+	The entry 5i4r is ON HOLD until Paper Publication

	Authors: Michalska, K., Stols, L., Eschenfeldt, W., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)		Authors: Michalska, K., Stols, L., Eschenfeldt, W., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)

OCA: Protected "5i4r" [edit=sysop:move=sysop]

OCA — Fri, 26 Feb 2016 16:46:09 GMT

Protected "5i4r" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:46, 26 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i4r is ON HOLD Authors: Michalska, K., Stols, L., Eschenfeldt, W., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genom...

OCA — Fri, 26 Feb 2016 16:46:07 GMT

New page: '''Unreleased structure''' The entry 5i4r is ON HOLD Authors: Michalska, K., Stols, L., Eschenfeldt, W., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genom...

New page

'''Unreleased structure'''

The entry 5i4r is ON HOLD

Authors: Michalska, K., Stols, L., Eschenfeldt, W., Hayes, C.S., Goulding, C.W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)

Description: Contact-dependent inhibition system from Escherichia coli NC101 -ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)
[[Category: Unreleased Structures]]
[[Category: Michalska, K]]
[[Category: Stols, L]]
[[Category: Joachimiak, A]]
[[Category: Hayes, C.S]]
[[Category: Goulding, C.W]]
[[Category: Midwest Center For Structural Genomics (Mcsg), Structure-Function Analysis Of Polymorphic Cdi Toxin-Immunity Protein Complexes (Uc4cdi)]]
[[Category: Eschenfeldt, W]]