5keg - Revision history

OCA at 09:59, 27 September 2023

OCA — Wed, 27 Sep 2023 09:59:18 GMT

←Older revision		Revision as of 09:59, 27 September 2023
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	<StructureSection load='5keg' size='340' side='right'caption='[[5keg]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5keg' size='340' side='right'caption='[[5keg]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5keg]] is a 2 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=5KEG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KEG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5keg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=5KEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KEG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APOBEC3A ([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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5keg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5keg OCA], [~~http~~://pdbe.org/5keg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5keg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5keg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5keg 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=5keg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5keg OCA], [https://pdbe.org/5keg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5keg RCSB], [https://www.ebi.ac.uk/pdbsum/5keg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5keg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ABC3A_HUMAN ABC3A_HUMAN]] DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno-associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.<ref>PMID:10469298</ref> <ref>PMID:12859895</ref> <ref>PMID:16527742</ref> <ref>PMID:19461882</ref> <ref>PMID:20615867</ref> <ref>PMID:20062055</ref> <ref>PMID:21496894</ref> <ref>PMID:21460793</ref> <ref>PMID:21123384</ref> <ref>PMID:21368204</ref> <ref>PMID:22896697</ref> <ref>PMID:22457529</ref>	+	[https://www.uniprot.org/uniprot/ABC3A_HUMAN ABC3A_HUMAN] DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno-associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.<ref>PMID:10469298</ref> <ref>PMID:12859895</ref> <ref>PMID:16527742</ref> <ref>PMID:19461882</ref> <ref>PMID:20615867</ref> <ref>PMID:20062055</ref> <ref>PMID:21496894</ref> <ref>PMID:21460793</ref> <ref>PMID:21123384</ref> <ref>PMID:21368204</ref> <ref>PMID:22896697</ref> <ref>PMID:22457529</ref>
	<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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hilbert~~, B J~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Kouno, T]]	+	[[Category: Hilbert BJ]]
-	[[Category: Matsuo, H]]	+	[[Category: Kouno T]]
-	[[Category: Royer~~, W E~~]]	+	[[Category: Matsuo H]]
-	[[Category: Schiffer~~, C A~~]]	+	[[Category: Royer WE]]
-	[[Category: Silvas, T]]	+	[[Category: Schiffer CA]]
-	~~[[Category: Apobec3a]]~~	+	[[Category: Silvas T]]
-	~~[[Category: Dna cytidine deaminase complex with a substrate dna]]~~	+
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 12:11, 25 December 2019

OCA — Wed, 25 Dec 2019 12:11:34 GMT

←Older revision		Revision as of 12:11, 25 December 2019
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	==Crystal structure of APOBEC3A in complex with a single-stranded DNA==		==Crystal structure of APOBEC3A in complex with a single-stranded DNA==
-	<StructureSection load='5keg' size='340' side='right' caption='[[5keg]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5keg' size='340' side='right'caption='[[5keg]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5keg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KEG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5keg]] is a 2 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=5KEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KEG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APOBEC3A ([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=5keg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5keg OCA], [http://pdbe.org/5keg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5keg RCSB], [http://www.ebi.ac.uk/pdbsum/5keg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5keg 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=5keg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5keg OCA], [http://pdbe.org/5keg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5keg RCSB], [http://www.ebi.ac.uk/pdbsum/5keg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5keg ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Hilbert, B J]]		[[Category: Hilbert, B J]]
	[[Category: Kouno, T]]		[[Category: Kouno, T]]

OCA at 12:49, 10 May 2017

OCA — Wed, 10 May 2017 12:49:41 GMT

←Older revision		Revision as of 12:49, 10 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5keg is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of APOBEC3A in complex with a single-stranded DNA==
		+	<StructureSection load='5keg' size='340' side='right' caption='[[5keg]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5keg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KEG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5keg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5keg OCA], [http://pdbe.org/5keg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5keg RCSB], [http://www.ebi.ac.uk/pdbsum/5keg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5keg ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ABC3A_HUMAN ABC3A_HUMAN]] DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno-associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.<ref>PMID:10469298</ref> <ref>PMID:12859895</ref> <ref>PMID:16527742</ref> <ref>PMID:19461882</ref> <ref>PMID:20615867</ref> <ref>PMID:20062055</ref> <ref>PMID:21496894</ref> <ref>PMID:21460793</ref> <ref>PMID:21123384</ref> <ref>PMID:21368204</ref> <ref>PMID:22896697</ref> <ref>PMID:22457529</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 A. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.

-	~~Authors: Kouno~~, T., Hilbert, ~~B.J.~~, ~~Silvas~~, T., Royer, ~~W.E.~~, Matsuo, H., Schiffer~~, C~~.A.	+	Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.,Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N, Matsuo H, Schiffer CA Nat Commun. 2017 Apr 28;8:15024. doi: 10.1038/ncomms15024. PMID:28452355<ref>PMID:28452355</ref>

-	~~Description: Crystal structure of APOBEC3A in complex with~~ a ~~single-stranded DNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Matsuo, H]]~~	+	<div class="pdbe-citations 5keg" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Royer~~, ~~W.E~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hilbert, B J]]
	[[Category: Kouno, T]]		[[Category: Kouno, T]]
-	[[Category: Schiffer, C.A]]	+	[[Category: Matsuo, H]]
		+	[[Category: Royer, W E]]
		+	[[Category: Schiffer, C A]]
	[[Category: Silvas, T]]		[[Category: Silvas, T]]
-	[[Category: ~~Hilbert, B.J~~]]	+	[[Category: Apobec3a]]
		+	[[Category: Dna cytidine deaminase complex with a substrate dna]]
		+	[[Category: Hydrolase-dna complex]]

OCA at 10:15, 9 March 2017

OCA — Thu, 09 Mar 2017 10:15:25 GMT

←Older revision		Revision as of 10:15, 9 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Matsuo, H]]		[[Category: Matsuo, H]]
		+	[[Category: Royer, W.E]]
	[[Category: Kouno, T]]		[[Category: Kouno, T]]
	[[Category: Schiffer, C.A]]		[[Category: Schiffer, C.A]]
-	[[Category: Hilbert, B.J]]
-	[[Category: Royer, W.E]]
	[[Category: Silvas, T]]		[[Category: Silvas, T]]
		+	[[Category: Hilbert, B.J]]

OCA at 21:29, 23 June 2016

OCA — Thu, 23 Jun 2016 21:29:10 GMT

←Older revision		Revision as of 21:29, 23 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5keg is ON HOLD	+	The entry 5keg is ON HOLD until Paper Publication

-	Authors: ~~Takahide~~ Kouno, ~~Brendan J~~. Hilbert, ~~Tania~~ Silvas, ~~William E~~. Royer, ~~Hiroshi~~ Matsuo, ~~Celia A~~. Schiffer	+	Authors: Kouno, T., Hilbert, B.J., Silvas, T., Royer, W.E., Matsuo, H., Schiffer, C.A.

	Description: Crystal structure of APOBEC3A in complex with a single-stranded DNA		Description: Crystal structure of APOBEC3A in complex with a single-stranded DNA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Takahide~~ Kouno, ~~Brendan J~~. Hilbert, ~~Tania Silvas, William E~~. Royer, ~~Hiroshi Matsuo, Celia A~~. ~~Schiffer~~]]	+	[[Category: Matsuo, H]]
		+	[[Category: Kouno, T]]
		+	[[Category: Schiffer, C.A]]
		+	[[Category: Hilbert, B.J]]
		+	[[Category: Royer, W.E]]
		+	[[Category: Silvas, T]]

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

OCA — Mon, 20 Jun 2016 13:50:12 GMT

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

←Older revision

Revision as of 13:50, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5keg is ON HOLD Authors: Takahide Kouno, Brendan J. Hilbert, Tania Silvas, William E. Royer, Hiroshi Matsuo, Celia A. Schiffer Description: Crystal...

OCA — Mon, 20 Jun 2016 13:50:10 GMT

New page: '''Unreleased structure''' The entry 5keg is ON HOLD Authors: Takahide Kouno, Brendan J. Hilbert, Tania Silvas, William E. Royer, Hiroshi Matsuo, Celia A. Schiffer Description: Crystal...

New page

'''Unreleased structure'''

The entry 5keg is ON HOLD

Authors: Takahide Kouno, Brendan J. Hilbert, Tania Silvas, William E. Royer, Hiroshi Matsuo, Celia A. Schiffer

Description: Crystal structure of APOBEC3A in complex with a single-stranded DNA
[[Category: Unreleased Structures]]
[[Category: Takahide Kouno, Brendan J. Hilbert, Tania Silvas, William E. Royer, Hiroshi Matsuo, Celia A. Schiffer]]