7ebd - Revision history

OCA at 08:41, 17 October 2024

2024-10-17T08:41:40Z

← Older revision		Revision as of 08:41, 17 October 2024
Line 3:		Line 3:
	<StructureSection load='7ebd' size='340' side='right'caption='[[7ebd]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='7ebd' size='340' side='right'caption='[[7ebd]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7ebd]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBD FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</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]] 2.25Å</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</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'>[https://proteopedia.org/fgij/fg.htm?mol=7ebd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebd OCA], [https://pdbe.org/7ebd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebd RCSB], [https://www.ebi.ac.uk/pdbsum/7ebd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebd 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=7ebd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebd OCA], [https://pdbe.org/7ebd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebd RCSB], [https://www.ebi.ac.uk/pdbsum/7ebd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebd ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Mammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense c-di-GMP generated by the CD-NTase (cGAS/DncV-like nucleotidyltransferase) encoded in the same operon and signal suicide commitment as a defense strategy that restricts phage propagation. However, the precise binding mode of c-di-GMP to bacterial STING and the specific recognition mechanism are still elusive. Here, we determine two complex crystal structures of bacterial STING/c-di-GMP, which provide a clear picture of how c-di-GMP is distinguished from other cyclic dinucleotides. The protein-protein interactions further reveal the driving force behind filament formation of bacterial STING. Finally, we group the bacterial STING into two classes based on the conserved motif in beta-strand lid, which dictate their ligand specificity and oligomerization mechanism, and propose an evolution-based model that describes the transition from c-di-GMP-dependent signaling in bacteria to 2'3'-cGAMP-dependent signaling in eukaryotes.

	Crystal structure and functional implication of bacterial STING.,Ko TP, Wang YC, Yang CS, Hou MH, Chen CJ, Chiu YF, Chen Y Nat Commun. 2022 Jan 10;13(1):26. doi: 10.1038/s41467-021-26583-3. PMID:35013136<ref>PMID:35013136</ref>		==See Also==
			*[[Stimulator of interferon genes protein 3D structures\|Stimulator of interferon genes protein 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7ebd" style="background-color:#fffaf0;"></div>~~
	== ~~References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen, Y]]		[[Category: Chen Y]]
	[[Category: Hou, M H]]		[[Category: Hou M-H]]
	[[Category: Ko, T P]]		[[Category: Ko T-P]]
	[[Category: Wang, Y C]]		[[Category: Wang Y-C]]
	[[Category: Yang, C S]]		[[Category: Yang C-S]]
	~~[[Category: Antiviral pathway]]~~
	~~[[Category: Complex]]~~
	~~[[Category: Cyclic dinucleotide]]~~
	~~[[Category: Second messenger]]~~
	~~[[Category: Signaling protein~~]]

OCA at 07:37, 19 January 2022

2022-01-19T07:37:32Z

← Older revision		Revision as of 07:37, 19 January 2022
Line 1:		Line 1:

	==Bacterial STING in complex with c-di-GMP==		==Bacterial STING in complex with c-di-GMP==
	<StructureSection load='7ebd' size='340' side='right'caption='[[7ebd]]' scene=''>		<StructureSection load='7ebd' size='340' side='right'caption='[[7ebd]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ebd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBD FirstGlance]. <br>
	</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=7ebd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebd OCA], [https://pdbe.org/7ebd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebd RCSB], [https://www.ebi.ac.uk/pdbsum/7ebd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebd ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</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'>[https://proteopedia.org/fgij/fg.htm?mol=7ebd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebd OCA], [https://pdbe.org/7ebd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebd RCSB], [https://www.ebi.ac.uk/pdbsum/7ebd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebd ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Mammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense c-di-GMP generated by the CD-NTase (cGAS/DncV-like nucleotidyltransferase) encoded in the same operon and signal suicide commitment as a defense strategy that restricts phage propagation. However, the precise binding mode of c-di-GMP to bacterial STING and the specific recognition mechanism are still elusive. Here, we determine two complex crystal structures of bacterial STING/c-di-GMP, which provide a clear picture of how c-di-GMP is distinguished from other cyclic dinucleotides. The protein-protein interactions further reveal the driving force behind filament formation of bacterial STING. Finally, we group the bacterial STING into two classes based on the conserved motif in beta-strand lid, which dictate their ligand specificity and oligomerization mechanism, and propose an evolution-based model that describes the transition from c-di-GMP-dependent signaling in bacteria to 2'3'-cGAMP-dependent signaling in eukaryotes.

			Crystal structure and functional implication of bacterial STING.,Ko TP, Wang YC, Yang CS, Hou MH, Chen CJ, Chiu YF, Chen Y Nat Commun. 2022 Jan 10;13(1):26. doi: 10.1038/s41467-021-26583-3. PMID:35013136<ref>PMID:35013136</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7ebd" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen Y]]		[[Category: Chen, Y]]
	[[Category: Hou M-H]]		[[Category: Hou, M H]]
	[[Category: Ko T-P]]		[[Category: Ko, T P]]
	[[Category: Wang Y-C]]		[[Category: Wang, Y C]]
	[[Category: Yang C-S]]		[[Category: Yang, C S]]
			[[Category: Antiviral pathway]]
			[[Category: Complex]]
			[[Category: Cyclic dinucleotide]]
			[[Category: Second messenger]]
			[[Category: Signaling protein]]

OCA at 09:25, 15 September 2021

2021-09-15T09:25:52Z

← Older revision		Revision as of 09:25, 15 September 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7ebd is ~~ON HOLD until Paper Publication~~		==Bacterial STING in complex with c-di-GMP==
			<StructureSection load='7ebd' size='340' side='right'caption='[[7ebd]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EBD FirstGlance]. <br>
	~~Description~~:		</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=7ebd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ebd OCA], [https://pdbe.org/7ebd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ebd RCSB], [https://www.ebi.ac.uk/pdbsum/7ebd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ebd ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Chen Y]]
			[[Category: Hou M-H]]
			[[Category: Ko T-P]]
			[[Category: Wang Y-C]]
			[[Category: Yang C-S]]

OCA at 04:28, 7 April 2021

2021-04-07T04:28:48Z

← Older revision		Revision as of 04:28, 7 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7ebd is ON HOLD		The entry 7ebd is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7ebd" [edit=sysop:move=sysop]

2021-03-17T05:19:06Z

Protected "7ebd" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:19, 17 March 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7ebd is ON HOLD Authors: Description: Category: Unreleased Structures

2021-03-17T05:19:05Z

New page: '''Unreleased structure''' The entry 7ebd is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ebd is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]