8h2f - Revision history

OCA at 11:16, 14 March 2024

2024-03-14T11:16:52Z

←Older revision		Revision as of 11:16, 14 March 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8h2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h2f OCA], [https://pdbe.org/8h2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h2f RCSB], [https://www.ebi.ac.uk/pdbsum/8h2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h2f 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=8h2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h2f OCA], [https://pdbe.org/8h2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h2f RCSB], [https://www.ebi.ac.uk/pdbsum/8h2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h2f ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In the spacer acquisition stage of CRISPR-Cas immunity, spacer orientation and protospacer adjacent motif (PAM) removal are two prerequisites for functional spacer integration. Cas4 has been implicated in both processing the prespacer and determining the spacer orientation. In Cas4-lacking systems, host 3'-5' DnaQ family exonucleases were recently reported to play a Cas4-like role. However, the molecular details of DnaQ functions remain elusive. Here, we characterized the spacer acquisition of the adaptation module of the Streptococcus thermophilus type I-E system, in which a DnaQ domain naturally fuses with Cas2. We presented X-ray crystal structures and cryo-electron microscopy structures of this adaptation module. Our biochemical data showed that DnaQ trimmed PAM-containing and PAM-deficient overhangs with different efficiencies. Based on these results, we proposed a time-dependent model for DnaQ-mediated spacer acquisition to elucidate PAM removal and spacer orientation determination in Cas4-lacking CRISPR-Cas systems.
-
-	DnaQ mediates directional spacer acquisition in the CRISPR-Cas system by a time-dependent mechanism.,Tang D, Jia T, Luo Y, Mou B, Cheng J, Qi S, Yao S, Su Z, Yu Y, Chen Q Innovation (Camb). 2023 Aug 9;4(5):100495. doi: 10.1016/j.xinn.2023.100495. , eCollection 2023 Sep 11. PMID:37663930<ref>PMID:37663930</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8h2f" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:15, 20 September 2023

2023-09-20T18:15:49Z

←Older revision		Revision as of 18:15, 20 September 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8h2f is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of DnaQ domain in complex witn TMP of Streptococcus thermophilus strain DGCC 7710==
		+	<StructureSection load='8h2f' size='340' side='right'caption='[[8h2f]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8h2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_thermophilus_DGCC_7710 Streptococcus thermophilus DGCC 7710]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8H2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H2F FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.448Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TMP:THYMIDINE-5-PHOSPHATE'>TMP</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=8h2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h2f OCA], [https://pdbe.org/8h2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h2f RCSB], [https://www.ebi.ac.uk/pdbsum/8h2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h2f ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the spacer acquisition stage of CRISPR-Cas immunity, spacer orientation and protospacer adjacent motif (PAM) removal are two prerequisites for functional spacer integration. Cas4 has been implicated in both processing the prespacer and determining the spacer orientation. In Cas4-lacking systems, host 3'-5' DnaQ family exonucleases were recently reported to play a Cas4-like role. However, the molecular details of DnaQ functions remain elusive. Here, we characterized the spacer acquisition of the adaptation module of the Streptococcus thermophilus type I-E system, in which a DnaQ domain naturally fuses with Cas2. We presented X-ray crystal structures and cryo-electron microscopy structures of this adaptation module. Our biochemical data showed that DnaQ trimmed PAM-containing and PAM-deficient overhangs with different efficiencies. Based on these results, we proposed a time-dependent model for DnaQ-mediated spacer acquisition to elucidate PAM removal and spacer orientation determination in Cas4-lacking CRISPR-Cas systems.

-	~~Authors: Chen, Q~~., Yu, Y.	+	DnaQ mediates directional spacer acquisition in the CRISPR-Cas system by a time-dependent mechanism.,Tang D, Jia T, Luo Y, Mou B, Cheng J, Qi S, Yao S, Su Z, Yu Y, Chen Q Innovation (Camb). 2023 Aug 9;4(5):100495. doi: 10.1016/j.xinn.2023.100495. , eCollection 2023 Sep 11. PMID:37663930<ref>PMID:37663930</ref>

-	~~Description: Crystal structure~~ of ~~DnaQ domian in complex witn TMP~~ of ~~Streptococcus thermophilus strain DGCC 7710~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Yu, Y~~]]	+	<div class="pdbe-citations 8h2f" style="background-color:#fffaf0;"></div>
-	[[Category: Chen, Q]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Streptococcus thermophilus DGCC 7710]]
		+	[[Category: Chen Q]]
		+	[[Category: Yu Y]]

OCA at 18:19, 16 November 2022

2022-11-16T18:19:36Z

←Older revision		Revision as of 18:19, 16 November 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8h2f is ON HOLD	+	The entry 8h2f is ON HOLD until Paper Publication

	Authors: Chen, Q., Yu, Y.		Authors: Chen, Q., Yu, Y.

OCA: Protected "8h2f" [edit=sysop:move=sysop]

2022-10-19T17:44:13Z

Protected "8h2f" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:44, 19 October 2022

OCA: New page: '''Unreleased structure''' The entry 8h2f is ON HOLD Authors: Chen, Q., Yu, Y. Description: Crystal structure of DnaQ domian in complex witn TMP of Streptococcus thermophilus strain DG...

2022-10-19T17:44:10Z

New page: '''Unreleased structure''' The entry 8h2f is ON HOLD Authors: Chen, Q., Yu, Y. Description: Crystal structure of DnaQ domian in complex witn TMP of Streptococcus thermophilus strain DG...

New page

'''Unreleased structure'''

The entry 8h2f is ON HOLD

Authors: Chen, Q., Yu, Y.

Description: Crystal structure of DnaQ domian in complex witn TMP of Streptococcus thermophilus strain DGCC 7710
[[Category: Unreleased Structures]]
[[Category: Yu, Y]]
[[Category: Chen, Q]]