3zhm - Revision history

OCA at 11:02, 20 December 2023

OCA — Wed, 20 Dec 2023 11:02:01 GMT

←Older revision		Revision as of 11:02, 20 December 2023
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	<StructureSection load='3zhm' size='340' side='right'caption='[[3zhm]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3zhm' size='340' side='right'caption='[[3zhm]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zhm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bacteriophage_tp901~~-1 ~~Bacteriophage tp901~~-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zhm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_phage_TP901-1 Lactococcus phage TP901-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHM FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~3zhi~~\|~~3zhi~~]]~~</div>~~</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]] 2.6Å</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=3zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhm OCA], [https://pdbe.org/3zhm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhm RCSB], [https://www.ebi.ac.uk/pdbsum/3zhm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhm 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=3zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhm OCA], [https://pdbe.org/3zhm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhm RCSB], [https://www.ebi.ac.uk/pdbsum/3zhm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O48503_9CAUD O48503_9CAUD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacteriophage tp901~~-1]]	+	[[Category: Lactococcus phage TP901-1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Frandsen~~, K H~~]]	+	[[Category: Frandsen KH]]
-	[[Category: Leggio, L Lo]]	+	[[Category: Lo Leggio L]]
-	[[Category: Poulsen~~, J N~~]]	+	[[Category: Poulsen JN]]
-	[[Category: Rasmussen~~, K K]]~~	+	[[Category: Rasmussen KK]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription factor]]~~	+
-	~~[[Category: Transcription regulation~~]]	+

OCA at 05:46, 10 August 2022

OCA — Wed, 10 Aug 2022 05:46:51 GMT

←Older revision		Revision as of 05:46, 10 August 2022
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	==N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site==		==N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site==
-	<StructureSection load='3zhm' size='340' side='right' caption='[[3zhm]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='3zhm' size='340' side='right'caption='[[3zhm]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zhm]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacteriophage_tp901-1 Bacteriophage tp901-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZHM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zhm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_tp901-1 Bacteriophage tp901-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZHM FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhi\|3zhi]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zhi\|3zhi]]</div></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=3zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhm OCA], [~~http~~://pdbe.org/3zhm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3zhm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3zhm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhm 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=3zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhm OCA], [https://pdbe.org/3zhm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zhm RCSB], [https://www.ebi.ac.uk/pdbsum/3zhm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Bacteriophage tp901-1]]		[[Category: Bacteriophage tp901-1]]
		+	[[Category: Large Structures]]
	[[Category: Frandsen, K H]]		[[Category: Frandsen, K H]]
	[[Category: Leggio, L Lo]]		[[Category: Leggio, L Lo]]

OCA at 16:53, 2 January 2017

OCA — Mon, 02 Jan 2017 16:53:21 GMT

←Older revision		Revision as of 16:53, 2 January 2017
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		+
	==N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site==		==N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site==
	<StructureSection load='3zhm' size='340' side='right' caption='[[3zhm]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3zhm' size='340' side='right' caption='[[3zhm]], [[Resolution\|resolution]] 2.60Å' scene=''>
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	<table><tr><td colspan='2'>[[3zhm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_tp901-1 Bacteriophage tp901-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZHM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3zhm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_tp901-1 Bacteriophage tp901-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZHM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhi\|3zhi]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhi\|3zhi]]</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=3zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhm RCSB], [http://www.ebi.ac.uk/pdbsum/3zhm 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=3zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhm OCA], [http://pdbe.org/3zhm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zhm RCSB], [http://www.ebi.ac.uk/pdbsum/3zhm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zhm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3zhm" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:18, 21 December 2014

OCA — Sun, 21 Dec 2014 16:18:03 GMT

←Older revision		Revision as of 16:18, 21 December 2014
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-	~~{{STRUCTURE_3zhm~~\| ~~PDB~~=3zhm \| ~~SCENE~~= }}	+	==N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site==
-	===N-terminal domain of the CI repressor from ~~bacteriophage~~ TP901-1 in complex with the ~~OL2~~ operator half-site~~===~~	+	<StructureSection load='3zhm' size='340' side='right' caption='[[3zhm]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24047404}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3zhm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_tp901-1 Bacteriophage tp901-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZHM FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zhi\|3zhi]]</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=3zhm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zhm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zhm RCSB], [http://www.ebi.ac.uk/pdbsum/3zhm PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In most temperate bacteriophages, regulation of the choice of lysogenic or lytic life cycle is controlled by a CI repressor protein. Inhibition of transcription is dependent on a helix-turn-helix motif, often located in the N-terminal domain (NTD), which binds to specific DNA sequences (operator sites). Here the crystal structure of the NTD of the CI repressor from phage TP901-1 has been determined at 1.6 A resolution, and at 2.6 A resolution in complex with a 9 bp double-stranded DNA fragment that constitutes a half-site of the OL operator. This N-terminal construct, comprising residues 2-74 of the CI repressor, is monomeric in solution as shown by nuclear magnetic resonance (NMR), small angle X-ray scattering, and gel filtration and is monomeric in the crystal structures. The binding interface between the NTD and the half-site in the crystal is very similar to the interface that can be mapped by NMR in solution with a full palindromic site. The interactions seen in the complexes (in the crystal and in solution) explain the observed affinity for the OR site that is lower than that for the OL site and the specificity for the recognized DNA sequence in comparison to that for other repressors. Compared with many well-studied phage repressor systems, the NTD from TP901-1 CI has a longer extended scaffolding helix that, interestingly, is strongly conserved in putative repressors of Gram-positive pathogens. On the basis of sequence comparisons, we suggest that these bacteria also possess repressor/antirepressor systems similar to that found in phage TP901-1.

-	~~==About this Structure==~~	+	Binding of the N-terminal domain of the lactococcal bacteriophage TP901-1 CI repressor to its target DNA: a crystallography, small angle scattering, and nuclear magnetic resonance study.,Frandsen KH, Rasmussen KK, Jensen MR, Hammer K, Pedersen M, Poulsen JC, Arleth L, Lo Leggio L Biochemistry. 2013 Oct 1;52(39):6892-904. doi: 10.1021/bi400439y. Epub 2013 Sep, 18. PMID:24047404<ref>PMID:24047404</ref>
-	~~[[3zhm]] is~~ a ~~3 chain structure~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann.ac~~.il/~~oca-bin/ocashort?id=3ZHM OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024047404</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Frandsen, K H.]]	+	== References ==
-	[[Category: Leggio, L Lo.]]	+	<references/>
-	[[Category: Poulsen, J N.]]	+	__TOC__
-	[[Category: Rasmussen, K K.]]	+	</StructureSection>
		+	[[Category: Bacteriophage tp901-1]]
		+	[[Category: Frandsen, K H]]
		+	[[Category: Leggio, L Lo]]
		+	[[Category: Poulsen, J N]]
		+	[[Category: Rasmussen, K K]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription factor]]		[[Category: Transcription factor]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]

OCA at 10:13, 25 December 2013

OCA — Wed, 25 Dec 2013 10:13:58 GMT

←Older revision		Revision as of 10:13, 25 December 2013
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3zhm\| PDB=3zhm \| SCENE= }}
		+	===N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site===
		+	{{ABSTRACT_PUBMED_24047404}}

-	~~The entry~~ 3zhm is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[3zhm]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZHM OCA].

-	~~Authors~~: Frandsen, K.H., ~~Rasmussen, K~~.~~K.,~~ Poulsen, J.N., ~~Lo Leggio, L~~.	+	==Reference==
-		+	<ref group="xtra">PMID:024047404</ref><references group="xtra"/><references/>
-	~~Description~~: ~~N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site~~	+	[[Category: Frandsen, K H.]]
		+	[[Category: Leggio, L Lo.]]
		+	[[Category: Poulsen, J N.]]
		+	[[Category: Rasmussen, K K.]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription factor]]
		+	[[Category: Transcription regulation]]

OCA at 09:26, 4 September 2013

OCA — Wed, 04 Sep 2013 09:26:28 GMT

←Older revision		Revision as of 09:26, 4 September 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3zhm is ON HOLD	+	The entry 3zhm is ON HOLD until Paper Publication

	Authors: Frandsen, K.H., Rasmussen, K.K., Poulsen, J.N., Lo Leggio, L.		Authors: Frandsen, K.H., Rasmussen, K.K., Poulsen, J.N., Lo Leggio, L.

	Description: N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site		Description: N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site

OCA: Protected "3zhm" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 08:40:37 GMT

Protected "3zhm" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:40, 2 January 2013

OCA: New page: '''Unreleased structure''' The entry 3zhm is ON HOLD Authors: Frandsen, K.H., Rasmussen, K.K., Poulsen, J.N., Lo Leggio, L. Description: N-terminal domain of the CI repressor from bact...

OCA — Wed, 02 Jan 2013 08:40:36 GMT

New page: '''Unreleased structure''' The entry 3zhm is ON HOLD Authors: Frandsen, K.H., Rasmussen, K.K., Poulsen, J.N., Lo Leggio, L. Description: N-terminal domain of the CI repressor from bact...

New page

'''Unreleased structure'''

The entry 3zhm is ON HOLD

Authors: Frandsen, K.H., Rasmussen, K.K., Poulsen, J.N., Lo Leggio, L.

Description: N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site