4u29 - Revision history

OCA: Redirecting to 4yir

2015-03-11T11:42:05Z

Redirecting to 4yir

←Older revision		Revision as of 11:42, 11 March 2015
Line 1:		Line 1:
-	~~==Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex==~~	+	#REDIRECT [[4yir]] This PDB entry is obsolete and replaced by 4yir
-	~~<StructureSection load='4u29' size='340' side='right' caption='~~[[~~4u29]], [[Resolution\|resolution]] 3.05Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[4u29~~]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U29 FirstGlance]. <br>	+
-	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=G47:N2-ETHANETHIOL-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>G47</scene></td></tr>	+
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qsf\|2qsf]], [[2qsg\|2qsg]], [[2qsh\|2qsh]]</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=4u29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u29 RCSB], [http://www.ebi.ac.uk/pdbsum/4u29 PDBsum]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Function ==~~	+
-	[[http://www.uniprot.org/uniprot/RAD4_YEAST RAD4_YEAST]] Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. [[http://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by ~~damage-processing enzymes.~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.	+
-		+
-	Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.,Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH Nat Commun. 2015 Jan 6;6:5849. doi: 10.1038/ncomms6849. PMID:25562780<ref>PMID:25562780</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Chen, X]]~~	+
-	~~[[Category: Kim, Y]]~~	+
-	~~[[Category: Min, J H]]~~	+
-	~~[[Category: Beta-hairpin]]~~	+
-	~~[[Category: Disulfide crosslinking]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna damage repair]]~~	+
-	~~[[Category: Nucleotide excision repair]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Protein-dna crosslinking]]~~	+
-	~~[[Category: Protein-dna interaction]]~~	+
-	~~[[Category: Transglutaminase domain]]~~	+
-	~~[[Category: Xeroderma pigmentosum]]~~	+

OCA at 11:26, 4 March 2015

2015-03-04T11:26:41Z

←Older revision		Revision as of 11:26, 4 March 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex==
		+	<StructureSection load='4u29' size='340' side='right' caption='[[4u29]], [[Resolution\|resolution]] 3.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4u29]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U29 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=G47:N2-ETHANETHIOL-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>G47</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2qsf\|2qsf]], [[2qsg\|2qsg]], [[2qsh\|2qsh]]</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=4u29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u29 RCSB], [http://www.ebi.ac.uk/pdbsum/4u29 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RAD4_YEAST RAD4_YEAST]] Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. [[http://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.

-	~~The entry 4u29 is ON HOLD~~	+	Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.,Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH Nat Commun. 2015 Jan 6;6:5849. doi: 10.1038/ncomms6849. PMID:25562780<ref>PMID:25562780</ref>

-	~~Authors: Min~~, J.-H.~~, Chen, X., Kim, Y~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	~~[[Category: Min, J.-H]]~~	+	__TOC__
		+	</StructureSection>
	[[Category: Chen, X]]		[[Category: Chen, X]]
	[[Category: Kim, Y]]		[[Category: Kim, Y]]
		+	[[Category: Min, J H]]
		+	[[Category: Beta-hairpin]]
		+	[[Category: Disulfide crosslinking]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna damage repair]]
		+	[[Category: Nucleotide excision repair]]
		+	[[Category: Protein-dna complex]]
		+	[[Category: Protein-dna crosslinking]]
		+	[[Category: Protein-dna interaction]]
		+	[[Category: Transglutaminase domain]]
		+	[[Category: Xeroderma pigmentosum]]

OCA at 18:03, 24 December 2014

2014-12-24T18:03:49Z

←Older revision		Revision as of 18:03, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex		Description: Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex
		+	[[Category: Unreleased Structures]]
		+	[[Category: Min, J.-H]]
		+	[[Category: Chen, X]]
		+	[[Category: Kim, Y]]

OCA: Protected "4u29" [edit=sysop:move=sysop]

2014-07-23T07:26:29Z

Protected "4u29" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:26, 23 July 2014

OCA: New page: '''Unreleased structure''' The entry 4u29 is ON HOLD Authors: Min, J.-H., Chen, X., Kim, Y. Description: Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex

2014-07-23T07:26:28Z

New page: '''Unreleased structure''' The entry 4u29 is ON HOLD Authors: Min, J.-H., Chen, X., Kim, Y. Description: Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex

New page

'''Unreleased structure'''

The entry 4u29 is ON HOLD

Authors: Min, J.-H., Chen, X., Kim, Y.

Description: Crystal structure of Rad4-Rad23 crosslinked to a normal DNA duplex