6nfk - Revision history

OCA at 06:52, 11 October 2023

OCA — Wed, 11 Oct 2023 06:52:43 GMT

←Older revision		Revision as of 06:52, 11 October 2023
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	<StructureSection load='6nfk' size='340' side='right'caption='[[6nfk]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='6nfk' size='340' side='right'caption='[[6nfk]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nfk]] 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=6NFK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NFK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nfk]] 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=6NFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NFK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 1.86Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>APOBEC3B ([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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/Single-stranded_DNA_cytosine_deaminase Single-stranded DNA cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.38 3.5.4.38] </~~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=6nfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfk OCA], [https://pdbe.org/6nfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nfk RCSB], [https://www.ebi.ac.uk/pdbsum/6nfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfk 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=6nfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfk OCA], [~~http~~://pdbe.org/6nfk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nfk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nfk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ABC3B_HUMAN ABC3B_HUMAN]] DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.<ref>PMID:12859895</ref> <ref>PMID:15466872</ref> <ref>PMID:16060832</ref> <ref>PMID:16527742</ref> <ref>PMID:20062055</ref> <ref>PMID:22457529</ref>	+	[https://www.uniprot.org/uniprot/ABC3G_HUMAN ABC3G_HUMAN] DNA deaminase (cytidine deaminase) that mediates a form of innate resistance to retroviral infections (at least to HIV-1 infection) by triggering G-to-A hypermutation in the newly synthesized viral DNA. The replacements C-to-U in the minus strand DNA of HIV-1 during reverse transcription, leads to G-to-A transitions in the plus strand. The inhibition of viral replication is either due to the degradation of the minus strand before its integration or to the lethality of the hypermutations. Modification of both DNA strands is not excluded. This antiviral activity is neutralized by the virion infectivity factor (VIF), that prevents the incorporation of APOBEC3G into progeny HIV-1 virions by both inhibiting its translation and/or by inducing its ubiquitination and subsequent degradation by the 26S proteasome. May also prevent the transposition of a subset of retroelements. Binds a variety of RNAs, but does not display detectable APOB, NF1 and NAT1 mRNA editing.<ref>PMID:14557625</ref> <ref>PMID:12167863</ref> <ref>PMID:12808466</ref> <ref>PMID:12809610</ref> <ref>PMID:12808465</ref> <ref>PMID:12859895</ref> <ref>PMID:12970355</ref> <ref>PMID:14528300</ref> <ref>PMID:15031497</ref> <ref>PMID:16527742</ref> <ref>PMID:21123384</ref> <ref>PMID:18288108</ref> [https://www.uniprot.org/uniprot/ABC3B_HUMAN ABC3B_HUMAN] DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.<ref>PMID:12859895</ref> <ref>PMID:15466872</ref> <ref>PMID:16060832</ref> <ref>PMID:16527742</ref> <ref>PMID:20062055</ref> <ref>PMID:22457529</ref>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Single-stranded DNA cytosine deaminase]]~~	+	[[Category: Aihara H]]
-	[[Category: Aihara, H]]	+	[[Category: Orellana K]]
-	[[Category: Orellana, K]]	+	[[Category: Shi K]]
-	[[Category: Shi, K]]	+
-	~~[[Category: Apobec]]~~	+
-	~~[[Category: Deaminase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 16:14, 29 January 2020

OCA — Wed, 29 Jan 2020 16:14:08 GMT

←Older revision		Revision as of 16:14, 29 January 2020
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	<StructureSection load='6nfk' size='340' side='right'caption='[[6nfk]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='6nfk' size='340' side='right'caption='[[6nfk]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nfk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NFK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nfk]] 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=6NFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NFK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APOBEC3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Single-stranded_DNA_cytosine_deaminase Single-stranded DNA cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.38 3.5.4.38] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Single-stranded_DNA_cytosine_deaminase Single-stranded DNA cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.38 3.5.4.38] </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=6nfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfk OCA], [http://pdbe.org/6nfk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nfk RCSB], [http://www.ebi.ac.uk/pdbsum/6nfk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfk 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=6nfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfk OCA], [http://pdbe.org/6nfk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nfk RCSB], [http://www.ebi.ac.uk/pdbsum/6nfk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfk ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Single-stranded DNA cytosine deaminase]]		[[Category: Single-stranded DNA cytosine deaminase]]

OCA at 09:07, 25 December 2019

OCA — Wed, 25 Dec 2019 09:07:44 GMT

←Older revision		Revision as of 09:07, 25 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6nfk is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G bound to iodide==
-		+	<StructureSection load='6nfk' size='340' side='right'caption='[[6nfk]], [[Resolution\|resolution]] 1.86Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6nfk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NFK FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Single-stranded_DNA_cytosine_deaminase Single-stranded DNA cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.38 3.5.4.38] </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=6nfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfk OCA], [http://pdbe.org/6nfk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nfk RCSB], [http://www.ebi.ac.uk/pdbsum/6nfk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ABC3B_HUMAN ABC3B_HUMAN]] DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.<ref>PMID:12859895</ref> <ref>PMID:15466872</ref> <ref>PMID:16060832</ref> <ref>PMID:16527742</ref> <ref>PMID:20062055</ref> <ref>PMID:22457529</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Single-stranded DNA cytosine deaminase]]
		+	[[Category: Aihara, H]]
		+	[[Category: Orellana, K]]
		+	[[Category: Shi, K]]
		+	[[Category: Apobec]]
		+	[[Category: Deaminase]]
		+	[[Category: Hydrolase]]

OCA at 06:30, 30 January 2019

OCA — Wed, 30 Jan 2019 06:30:26 GMT

←Older revision		Revision as of 06:30, 30 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6nfk is ON HOLD	+	The entry 6nfk is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6nfk" [edit=sysop:move=sysop]

OCA — Wed, 26 Dec 2018 06:52:06 GMT

Protected "6nfk" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:52, 26 December 2018

OCA: New page: '''Unreleased structure''' The entry 6nfk is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Dec 2018 06:52:05 GMT

New page: '''Unreleased structure''' The entry 6nfk is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6nfk is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]