5itm - Revision history

OCA at 09:17, 20 March 2024

OCA — Wed, 20 Mar 2024 09:17:06 GMT

←Older revision		Revision as of 09:17, 20 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A0E3K9N8_SACSO A0A0E3K9N8_SACSO]		[https://www.uniprot.org/uniprot/A0A0E3K9N8_SACSO A0A0E3K9N8_SACSO]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 A, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22' and R11'/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.
-
-	The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA.,Lin BL, Chen CY, Huang CH, Ko TP, Chiang CH, Lin KF, Chang YC, Lin PY, Tsai HG, Wang AH PLoS One. 2017 Jan 9;12(1):e0169627. doi: 10.1371/journal.pone.0169627., eCollection 2017. PMID:28068385<ref>PMID:28068385</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5itm" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:09, 30 August 2023

OCA — Wed, 30 Aug 2023 14:09:04 GMT

←Older revision		Revision as of 14:09, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='5itm' size='340' side='right'caption='[[5itm]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5itm' size='340' side='right'caption='[[5itm]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5itm]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_35091 Atcc 35091~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ITM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5itm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ITM FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5itj\|5itj]]</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]] 1.4Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">SULA_1064, SULB_1065, SULC_1064 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=2287 ATCC 35091])~~</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=5itm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5itm OCA], [https://pdbe.org/5itm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5itm RCSB], [https://www.ebi.ac.uk/pdbsum/5itm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5itm 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=5itm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5itm OCA], [~~http~~://pdbe.org/5itm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5itm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5itm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5itm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0E3K9N8_SACSO A0A0E3K9N8_SACSO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 35091]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang~~, Y C~~]]	+	[[Category: Saccharolobus solfataricus]]
-	[[Category: Chen~~, C Y~~]]	+	[[Category: Chang YC]]
-	[[Category: Chiang~~, C H~~]]	+	[[Category: Chen CY]]
-	[[Category: Huang~~, C H~~]]	+	[[Category: Chiang CH]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Huang CH]]
-	[[Category: Lin~~, B L~~]]	+	[[Category: Ko TP]]
-	[[Category: Lin~~, K F~~]]	+	[[Category: Lin BL]]
-	[[Category: Lin~~, P Y~~]]	+	[[Category: Lin KF]]
-	[[Category: Tsai~~, H H.G~~]]	+	[[Category: Lin PY]]
-	[[Category: Wang~~, A H.J]]~~	+	[[Category: Tsai HHG]]
-	~~[[Category: Complex]]~~	+	[[Category: Wang AHJ]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna-binding fold]]~~	+
-	~~[[Category: Histone-like protein~~]]	+

OCA at 07:31, 3 June 2020

OCA — Wed, 03 Jun 2020 07:31:21 GMT

←Older revision		Revision as of 07:31, 3 June 2020
Line 1:		Line 1:

	==The structure of truncated histone-like protein==		==The structure of truncated histone-like protein==
-	<StructureSection load='5itm' size='340' side='right' caption='[[5itm]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5itm' size='340' side='right'caption='[[5itm]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5itm]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ITM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5itm]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ITM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5itj\|5itj]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5itj\|5itj]]</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=5itm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5itm OCA], [http://pdbe.org/5itm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5itm RCSB], [http://www.ebi.ac.uk/pdbsum/5itm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5itm ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SULA_1064, SULB_1065, SULC_1064 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</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=5itm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5itm OCA], [http://pdbe.org/5itm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5itm RCSB], [http://www.ebi.ac.uk/pdbsum/5itm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5itm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 35091]]
		+	[[Category: Large Structures]]
	[[Category: Chang, Y C]]		[[Category: Chang, Y C]]
	[[Category: Chen, C Y]]		[[Category: Chen, C Y]]

OCA at 23:29, 25 January 2017

OCA — Wed, 25 Jan 2017 23:29:14 GMT

←Older revision		Revision as of 23:29, 25 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5itm is ~~ON HOLD until Paper~~ Publication	+	==The structure of truncated histone-like protein==
		+	<StructureSection load='5itm' size='340' side='right' caption='[[5itm]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5itm]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ITM FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5itj\|5itj]]</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=5itm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5itm OCA], [http://pdbe.org/5itm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5itm RCSB], [http://www.ebi.ac.uk/pdbsum/5itm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5itm ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 A, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22' and R11'/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.

-	~~Authors:~~ Lin~~, B.L.~~, Chen~~, C.Y.~~, Huang~~, C.H.~~, Ko~~, T.P.~~, Chiang, ~~C.H.~~, ~~Ho, M.R.~~, Lin, K.F.~~, Chang, Y~~.C.~~, Sue, S~~.C., ~~Wang, A.H~~.	+	The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA.,Lin BL, Chen CY, Huang CH, Ko TP, Chiang CH, Lin KF, Chang YC, Lin PY, Tsai HG, Wang AH PLoS One. 2017 Jan 9;12(1):e0169627. doi: 10.1371/journal.pone.0169627., eCollection 2017. PMID:28068385<ref>PMID:28068385</ref>

-	~~Description: The structure~~ of ~~truncated histone~~-~~like protein~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Ho, ~~M.R~~]]	+	<div class="pdbe-citations 5itm" style="background-color:#fffaf0;"></div>
-	[[Category: Ko, T.P]]	+	== References ==
-	[[Category: Lin, B.L]]	+	<references/>
-	[[Category: ~~Wang~~, ~~A.H~~]]	+	__TOC__
-	[[Category: ~~Huang~~, ~~C.H~~]]	+	</StructureSection>
-	[[Category: ~~Sue~~, S.C]]	+	[[Category: Chang, Y C]]
-	[[Category: ~~Lin~~, K.F]]	+	[[Category: Chen, C Y]]
-	[[Category: ~~Chang, Y.C~~]]	+	[[Category: Chiang, C H]]
-	[[Category: ~~Chen, C.Y~~]]	+	[[Category: Huang, C H]]
-	[[Category: ~~Chiang, C.H~~]]	+	[[Category: Ko, T P]]
		+	[[Category: Lin, B L]]
		+	[[Category: Lin, K F]]
		+	[[Category: Lin, P Y]]
		+	[[Category: Tsai, H H.G]]
		+	[[Category: Wang, A H.J]]
		+	[[Category: Complex]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna-binding fold]]
		+	[[Category: Histone-like protein]]

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

OCA — Wed, 11 May 2016 00:55:54 GMT

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

←Older revision

Revision as of 00:55, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5itm is ON HOLD until Paper Publication Authors: Lin, B.L., Chen, C.Y., Huang, C.H., Ko, T.P., Chiang, C.H., Ho, M.R., Lin, K.F., Chang, Y.C., Sue, ...

OCA — Wed, 11 May 2016 00:55:53 GMT

New page: '''Unreleased structure''' The entry 5itm is ON HOLD until Paper Publication Authors: Lin, B.L., Chen, C.Y., Huang, C.H., Ko, T.P., Chiang, C.H., Ho, M.R., Lin, K.F., Chang, Y.C., Sue, ...

New page

'''Unreleased structure'''

The entry 5itm is ON HOLD until Paper Publication

Authors: Lin, B.L., Chen, C.Y., Huang, C.H., Ko, T.P., Chiang, C.H., Ho, M.R., Lin, K.F., Chang, Y.C., Sue, S.C., Wang, A.H.

Description: The structure of truncated histone-like protein
[[Category: Unreleased Structures]]
[[Category: Ho, M.R]]
[[Category: Ko, T.P]]
[[Category: Lin, B.L]]
[[Category: Wang, A.H]]
[[Category: Huang, C.H]]
[[Category: Sue, S.C]]
[[Category: Lin, K.F]]
[[Category: Chang, Y.C]]
[[Category: Chen, C.Y]]
[[Category: Chiang, C.H]]