5ko9 - Revision history

OCA at 10:49, 27 September 2023

OCA — Wed, 27 Sep 2023 10:49:49 GMT

←Older revision		Revision as of 10:49, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5ko9' size='340' side='right'caption='[[5ko9]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5ko9' size='340' side='right'caption='[[5ko9]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ko9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KO9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ko9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KO9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 1.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HMCES, C3orf37, DC12, SRAPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=5ko9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko9 OCA], [~~http~~://pdbe.org/5ko9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ko9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ko9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko9 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=5ko9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko9 OCA], [https://pdbe.org/5ko9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ko9 RCSB], [https://www.ebi.ac.uk/pdbsum/5ko9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HMCES_HUMAN HMCES_HUMAN]] Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).<ref>PMID:23945014</ref>	+	[https://www.uniprot.org/uniprot/HMCES_HUMAN HMCES_HUMAN] Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).<ref>PMID:23945014</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Bountra, C]]	+	[[Category: Bountra C]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Edwards AM]]
-	[[Category: Halabelian, L]]	+	[[Category: Halabelian L]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Srap domain~~]]	+

OCA at 11:22, 13 November 2019

OCA — Wed, 13 Nov 2019 11:22:45 GMT

←Older revision		Revision as of 11:22, 13 November 2019
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/HMCES_HUMAN HMCES_HUMAN]] Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).<ref>PMID:23945014</ref>		[[http://www.uniprot.org/uniprot/HMCES_HUMAN HMCES_HUMAN]] Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).<ref>PMID:23945014</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA. HMCES interacts with both single-strand and duplex segments of DNA, with two independent duplex DNA interaction sites identified in the SRAP domain. The HMCES DNA-protein cross-link structure provides structural insights into a novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys 2 of HMCES. Collectively, our structures demonstrate the capacity for the SRAP domain to interact with a variety of single-strand- and double-strand-containing DNA structures found in DNA-damage sites, including 5' and 3' overhang DNAs and gapped DNAs with short single-strand segments.
		+
		+	Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.,Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH Nat Struct Mol Biol. 2019 Jul;26(7):607-612. doi: 10.1038/s41594-019-0246-6. Epub, 2019 Jun 24. PMID:31235913<ref>PMID:31235913</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ko9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:18, 26 June 2019

OCA — Wed, 26 Jun 2019 07:18:21 GMT

←Older revision		Revision as of 07:18, 26 June 2019
Line 1:		Line 1:

	==Crystal Structure of the SRAP Domain of Human HMCES Protein==		==Crystal Structure of the SRAP Domain of Human HMCES Protein==
-	<StructureSection load='5ko9' size='340' side='right' caption='[[5ko9]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5ko9' size='340' side='right'caption='[[5ko9]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ko9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KO9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ko9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KO9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMCES, C3orf37, DC12, SRAPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5ko9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko9 OCA], [http://pdbe.org/5ko9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ko9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ko9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko9 ProSAT]</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=5ko9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko9 OCA], [http://pdbe.org/5ko9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ko9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ko9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko9 ProSAT]</span></td></tr>
	</table>		</table>
Line 13:		Line 14:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 06:54, 10 September 2016

OCA — Sat, 10 Sep 2016 06:54:41 GMT

←Older revision		Revision as of 06:54, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ko9 is ~~ON HOLD until Aug 24 2017~~	+	==Crystal Structure of the SRAP Domain of Human HMCES Protein==
-		+	<StructureSection load='5ko9' size='340' side='right' caption='[[5ko9]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~Authors~~: ~~Halabelian, L~~., ~~Li, Y~~., ~~Bountra, C~~., ~~Edwards, A~~.M., ~~Arrowsmith, C~~.H., ~~Structural Genomics Consortium (SGC)~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ko9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KO9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KO9 FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure~~ of ~~the SRAP Domain of Human HMCES Protein~~ (~~CASP target~~)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5ko9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ko9 OCA], [http://pdbe.org/5ko9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ko9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ko9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ko9 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HMCES_HUMAN HMCES_HUMAN]] Specifically binds 5-hydroxymethylcytosine (5hmC)-containing DNA in stem cells, suggesting that it acts as a specific reader of 5hmC in stem cells (By similarity). May act as a peptidase; experimental evidences are however required to confirm this prediction (PubMed:23945014).<ref>PMID:23945014</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arrowsmith, C H]]
		+	[[Category: Bountra, C]]
		+	[[Category: Edwards, A M]]
		+	[[Category: Halabelian, L]]
	[[Category: Li, Y]]		[[Category: Li, Y]]
-	[[Category: ~~Halabelian, L~~]]	+	[[Category: Structural genomic]]
-	[[Category: ~~Bountra, C~~]]	+	[[Category: Dna binding protein]]
-	[[Category: ~~Arrowsmith, C.H~~]]	+	[[Category: Dna-binding]]
-	[[Category: ~~Edwards, A.M~~]]	+	[[Category: Sgc]]
-	[[Category: ~~Structural Genomics Consortium (Sgc)~~]]	+	[[Category: Srap domain]]

OCA at 13:11, 27 July 2016

OCA — Wed, 27 Jul 2016 13:11:11 GMT

←Older revision		Revision as of 13:11, 27 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ko9 is ON HOLD	+	The entry 5ko9 is ON HOLD until Aug 24 2017

	Authors: Halabelian, L., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)		Authors: Halabelian, L., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

OCA at 09:29, 14 July 2016

OCA — Thu, 14 Jul 2016 09:29:51 GMT

←Older revision		Revision as of 09:29, 14 July 2016
Line 3:		Line 3:
	The entry 5ko9 is ON HOLD		The entry 5ko9 is ON HOLD

-	Authors: Halabelian, L., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium	+	Authors: Halabelian, L., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

	Description: Crystal Structure of the SRAP Domain of Human HMCES Protein (CASP target)		Description: Crystal Structure of the SRAP Domain of Human HMCES Protein (CASP target)
Line 12:		Line 12:
	[[Category: Arrowsmith, C.H]]		[[Category: Arrowsmith, C.H]]
	[[Category: Edwards, A.M]]		[[Category: Edwards, A.M]]
-	[[Category: Structural Genomics Consortium]]	+	[[Category: Structural Genomics Consortium (Sgc)]]

OCA: Protected "5ko9" [edit=sysop:move=sysop]

OCA — Wed, 13 Jul 2016 00:38:50 GMT

Protected "5ko9" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:38, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5ko9 is ON HOLD Authors: Halabelian, L., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium Description: Crystal ...

OCA — Wed, 13 Jul 2016 00:38:49 GMT

New page: '''Unreleased structure''' The entry 5ko9 is ON HOLD Authors: Halabelian, L., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium Description: Crystal ...

New page

'''Unreleased structure'''

The entry 5ko9 is ON HOLD

Authors: Halabelian, L., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium

Description: Crystal Structure of the SRAP Domain of Human HMCES Protein (CASP target)
[[Category: Unreleased Structures]]
[[Category: Li, Y]]
[[Category: Halabelian, L]]
[[Category: Bountra, C]]
[[Category: Arrowsmith, C.H]]
[[Category: Edwards, A.M]]
[[Category: Structural Genomics Consortium]]