5fhe - Revision history

OCA at 09:12, 20 March 2024

2024-03-20T09:12:06Z

←Older revision		Revision as of 09:12, 20 March 2024
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [https://pdbe.org/5fhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [https://www.ebi.ac.uk/pdbsum/5fhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhe 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=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [https://pdbe.org/5fhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [https://www.ebi.ac.uk/pdbsum/5fhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhe ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Pif1 is a conserved SF1B DNA helicase involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. Here, we report the structures of the helicase domain of human Pif1 and Bacteroides sp Pif1 (BaPif1) in complex with ADP-AlF4(-) and two different single-stranded DNAs (ssDNAs). The wedge region equivalent to the beta hairpin in other SF1B DNA helicases folds into an extended loop followed by an alpha helix. The Pif1 signature motif of BaPif1 interacts with the wedge region and a short helix in order to stabilize these ssDNA binding elements, therefore indirectly exerting its functional role. Domain 2B of BaPif1 undergoes a large conformational change upon concomitant binding of ATP and ssDNA, which is critical for Pif1's activities. BaPif1 cocrystallized with a tailed dsDNA and ADP-AlF4(-), resulting in a bound ssDNA bent nearly 90 degrees at the ssDNA/dsDNA junction. The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity of Pif1.
-
-	Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1.,Zhou X, Ren W, Bharath SR, Tang X, He Y, Chen C, Liu Z, Li D, Song H Cell Rep. 2016 Mar 1;14(8):2030-9. doi: 10.1016/j.celrep.2016.02.008. Epub 2016, Feb 18. PMID:26904952<ref>PMID:26904952</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5fhe" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:51, 19 July 2023

2023-07-19T06:51:19Z

←Older revision		Revision as of 06:51, 19 July 2023
Line 3:		Line 3:
	<StructureSection load='5fhe' size='340' side='right'caption='[[5fhe]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5fhe' size='340' side='right'caption='[[5fhe]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fhe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FHE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fhe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FHE FirstGlance]. <br>
-	</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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fhd\|5fhd]], [[5fhf\|5fhf]], [[5fhg\|5fhg]], [[5fhh\|5fhh]]~~</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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [~~http~~://pdbe.org/5fhe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fhe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhe 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=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [https://pdbe.org/5fhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [https://www.ebi.ac.uk/pdbsum/5fhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhe ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides fragilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bharath~~, S R~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Ren, W]]	+	[[Category: Bharath SR]]
-	[[Category: Song, H]]	+	[[Category: Ren W]]
-	[[Category: Zhou, X]]	+	[[Category: Song H]]
-	~~[[Category: Dna helicase]]~~	+	[[Category: Zhou X]]
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Pif1 helicase~~]]	+

OCA at 07:19, 6 May 2020

2020-05-06T07:19:45Z

←Older revision		Revision as of 07:19, 6 May 2020
Line 1:		Line 1:

	==Crystal structure of Bacteroides Pif1 bound to ssDNA==		==Crystal structure of Bacteroides Pif1 bound to ssDNA==
-	<StructureSection load='5fhe' size='340' side='right' caption='[[5fhe]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5fhe' size='340' side='right'caption='[[5fhe]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fhe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FHE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fhe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FHE 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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fhd\|5fhd]], [[5fhf\|5fhf]], [[5fhg\|5fhg]], [[5fhh\|5fhh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fhd\|5fhd]], [[5fhf\|5fhf]], [[5fhg\|5fhg]], [[5fhh\|5fhh]]</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=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [http://pdbe.org/5fhe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [http://www.ebi.ac.uk/pdbsum/5fhe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhe 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=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [http://pdbe.org/5fhe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [http://www.ebi.ac.uk/pdbsum/5fhe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhe ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bharath, S R]]		[[Category: Bharath, S R]]
	[[Category: Ren, W]]		[[Category: Ren, W]]

OCA at 09:53, 27 September 2017

2017-09-27T09:53:35Z

←Older revision		Revision as of 09:53, 27 September 2017
Line 6:		Line 6:
	</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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fhd\|5fhd]], [[5fhf\|5fhf]], [[5fhg\|5fhg]], [[5fhh\|5fhh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fhd\|5fhd]], [[5fhf\|5fhf]], [[5fhg\|5fhg]], [[5fhh\|5fhh]]</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=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [http://pdbe.org/5fhe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [http://www.ebi.ac.uk/pdbsum/5fhe 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=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [http://pdbe.org/5fhe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [http://www.ebi.ac.uk/pdbsum/5fhe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fhe ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:34, 11 May 2016

2016-05-11T20:34:10Z

←Older revision		Revision as of 20:34, 11 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fhe is ~~ON HOLD~~	+	==Crystal structure of Bacteroides Pif1 bound to ssDNA==
		+	<StructureSection load='5fhe' size='340' side='right' caption='[[5fhe]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fhe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FHE 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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fhd\|5fhd]], [[5fhf\|5fhf]], [[5fhg\|5fhg]], [[5fhh\|5fhh]]</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=5fhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fhe OCA], [http://pdbe.org/5fhe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fhe RCSB], [http://www.ebi.ac.uk/pdbsum/5fhe PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pif1 is a conserved SF1B DNA helicase involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. Here, we report the structures of the helicase domain of human Pif1 and Bacteroides sp Pif1 (BaPif1) in complex with ADP-AlF4(-) and two different single-stranded DNAs (ssDNAs). The wedge region equivalent to the beta hairpin in other SF1B DNA helicases folds into an extended loop followed by an alpha helix. The Pif1 signature motif of BaPif1 interacts with the wedge region and a short helix in order to stabilize these ssDNA binding elements, therefore indirectly exerting its functional role. Domain 2B of BaPif1 undergoes a large conformational change upon concomitant binding of ATP and ssDNA, which is critical for Pif1's activities. BaPif1 cocrystallized with a tailed dsDNA and ADP-AlF4(-), resulting in a bound ssDNA bent nearly 90 degrees at the ssDNA/dsDNA junction. The conformational snapshots of BaPif1 provide insights into the mechanism governing the helicase activity of Pif1.

-	~~Authors: Zhou~~, X., Ren, W., Bharath, ~~S.R.~~, ~~Song~~, H.	+	Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1.,Zhou X, Ren W, Bharath SR, Tang X, He Y, Chen C, Liu Z, Li D, Song H Cell Rep. 2016 Mar 1;14(8):2030-9. doi: 10.1016/j.celrep.2016.02.008. Epub 2016, Feb 18. PMID:26904952<ref>PMID:26904952</ref>

-	~~Description: Crystal structure~~ of ~~Bacteroides Pif1 bound to ssDNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Zhou, X]]~~	+	<div class="pdbe-citations 5fhe" style="background-color:#fffaf0;"></div>
-	[[Category: Bharath, S.R]]	+	== References ==
-	~~[[Category: Song, H~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bharath, S R]]
	[[Category: Ren, W]]		[[Category: Ren, W]]
		+	[[Category: Song, H]]
		+	[[Category: Zhou, X]]
		+	[[Category: Dna helicase]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Pif1 helicase]]

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

2015-12-30T17:57:46Z

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

←Older revision

Revision as of 17:57, 30 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fhe is ON HOLD Authors: Zhou, X., Ren, W., Bharath, S.R., Song, H. Description: Crystal structure of Bacteroides Pif1 bound to ssDNA [[Category: U...

2015-12-30T17:57:45Z

New page: '''Unreleased structure''' The entry 5fhe is ON HOLD Authors: Zhou, X., Ren, W., Bharath, S.R., Song, H. Description: Crystal structure of Bacteroides Pif1 bound to ssDNA [[Category: U...

New page

'''Unreleased structure'''

The entry 5fhe is ON HOLD

Authors: Zhou, X., Ren, W., Bharath, S.R., Song, H.

Description: Crystal structure of Bacteroides Pif1 bound to ssDNA
[[Category: Unreleased Structures]]
[[Category: Zhou, X]]
[[Category: Bharath, S.R]]
[[Category: Song, H]]
[[Category: Ren, W]]