5zg9 - Revision history

OCA at 10:27, 27 March 2024

2024-03-27T10:27:48Z

←Older revision		Revision as of 10:27, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5zg9' size='340' side='right'caption='[[5zg9]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='5zg9' size='340' side='right'caption='[[5zg9]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zg9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZG9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZG9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zg9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyricularia_oryzae_P131 Pyricularia oryzae P131] 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=5ZG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZG9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.04Å</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=5zg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zg9 OCA], [~~http~~://pdbe.org/5zg9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zg9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zg9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zg9 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5zg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zg9 OCA], [https://pdbe.org/5zg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zg9 RCSB], [https://www.ebi.ac.uk/pdbsum/5zg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zg9 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/L7IX95_MAGOP L7IX95_MAGOP]
-	MoSub1 is an ortholog of yeast single stranded DNA binding protein Sub1 or human PC4 from rice blast fungus. All of them share a similar DNA binding region and may have similar biological roles. The well-studied Sub1/PC4 has been reported to play multiple roles in DNA metabolic processes, such as transcription and DNA repair and their DNA binding capacity is significantly affected by phosphorylation. Here, we determined the crystal structure of MoSub1 complexed with ssDNA in a phosphate solution. The crystal structure of the MoSub1-ssDNA complex was solved to a resolution of 2.04 A. A phosphate ion at the interface of the protein-DNA interaction of the complex bridged the lys84 of the protein and two nucleotides. The DNA was bound in novel mode (L mode) in the MoSub1 complex in the presence of phosphate ions, while DNA bound in the straight mode in the absence of the phosphate ion and in U mode in the same binding motif of the PC4-ssDNA complex. The crystal structure of the complex and a small-angle X-ray scattering analysis revealed that the phosphate ion at the protein-DNA interface affected the DNA binding mode of MoSub1 to oligo-DNA and provided a new structural clue for studying its functions.	+
-		+
-	The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus.,Zhao Y, Zhang Y, Huang J, Wang S, Yi L, Zhang X, Xu M, Fang X, Liu J Proteins. 2019 Apr;87(4):~~257-264. doi: 10.1002~~/~~prot.25647. Epub 2018 Dec 27. PMID:30561148<ref>PMID:30561148<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5zg9" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Huang, J~~]]	+	[[Category: Pyricularia oryzae P131]]
-	[[Category: ~~Liu, H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Liu,~~ J]]	+	[[Category: Huang J]]
-	[[Category: ~~Wang, S~~]]	+	[[Category: Liu H]]
-	[[Category: ~~Yi, L~~]]	+	[[Category: Liu J]]
-	[[Category: ~~Zhang, X~~]]	+	[[Category: Wang S]]
-	[[Category: ~~Zhao, Y~~]]	+	[[Category: Yi L]]
-	[[Category: ~~Dna binding protein~~]]	+	[[Category: Zhang X]]
-	[[Category: ~~Dna binding protein-dna complex]]~~	+	[[Category: Zhao Y]]
-	~~[[Category: Pc4-like protein]]~~	+
-	~~[[Category: Ssdna binding protein]]~~	+
-	~~[[Category: Transcriptional co-factor~~]]	+

OCA at 06:30, 27 March 2019

2019-03-27T06:30:26Z

←Older revision		Revision as of 06:30, 27 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zg9 is ~~ON HOLD~~	+	==Crystal structure of MoSub1-ssDNA complex in phosphate buffer==
		+	<StructureSection load='5zg9' size='340' side='right'caption='[[5zg9]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zg9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZG9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZG9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5zg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zg9 OCA], [http://pdbe.org/5zg9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zg9 RCSB], [http://www.ebi.ac.uk/pdbsum/5zg9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zg9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	MoSub1 is an ortholog of yeast single stranded DNA binding protein Sub1 or human PC4 from rice blast fungus. All of them share a similar DNA binding region and may have similar biological roles. The well-studied Sub1/PC4 has been reported to play multiple roles in DNA metabolic processes, such as transcription and DNA repair and their DNA binding capacity is significantly affected by phosphorylation. Here, we determined the crystal structure of MoSub1 complexed with ssDNA in a phosphate solution. The crystal structure of the MoSub1-ssDNA complex was solved to a resolution of 2.04 A. A phosphate ion at the interface of the protein-DNA interaction of the complex bridged the lys84 of the protein and two nucleotides. The DNA was bound in novel mode (L mode) in the MoSub1 complex in the presence of phosphate ions, while DNA bound in the straight mode in the absence of the phosphate ion and in U mode in the same binding motif of the PC4-ssDNA complex. The crystal structure of the complex and a small-angle X-ray scattering analysis revealed that the phosphate ion at the protein-DNA interface affected the DNA binding mode of MoSub1 to oligo-DNA and provided a new structural clue for studying its functions.

-	~~Authors~~:	+	The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus.,Zhao Y, Zhang Y, Huang J, Wang S, Yi L, Zhang X, Xu M, Fang X, Liu J Proteins. 2019 Apr;87(4):257-264. doi: 10.1002/prot.25647. Epub 2018 Dec 27. PMID:30561148<ref>PMID:30561148</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 5zg9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Huang, J]]
		+	[[Category: Liu, H]]
		+	[[Category: Liu, J]]
		+	[[Category: Wang, S]]
		+	[[Category: Yi, L]]
		+	[[Category: Zhang, X]]
		+	[[Category: Zhao, Y]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Pc4-like protein]]
		+	[[Category: Ssdna binding protein]]
		+	[[Category: Transcriptional co-factor]]

OCA: Protected "5zg9" [edit=sysop:move=sysop]

2018-03-14T05:02:12Z

Protected "5zg9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:02, 14 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zg9 is ON HOLD Authors: Description: Category: Unreleased Structures

2018-03-14T05:02:10Z

New page: '''Unreleased structure''' The entry 5zg9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5zg9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]