5tkm - Revision history

OCA at 13:04, 4 October 2023

OCA — Wed, 04 Oct 2023 13:04:33 GMT

←Older revision		Revision as of 13:04, 4 October 2023
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	<StructureSection load='5tkm' size='340' side='right'caption='[[5tkm]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5tkm' size='340' side='right'caption='[[5tkm]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tkm]] 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=5TKM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tkm]] is a 2 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=5TKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TKM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 1.9Å</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=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=5tkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tkm OCA], [~~http~~://pdbe.org/5tkm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tkm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tkm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tkm 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=5tkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tkm OCA], [https://pdbe.org/5tkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tkm RCSB], [https://www.ebi.ac.uk/pdbsum/5tkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tkm 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/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>
	<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: Arutiunian, V]]	+	[[Category: Arutiunian V]]
-	[[Category: Besse, G]]	+	[[Category: Besse G]]
-	[[Category: Chen~~, X S~~]]	+	[[Category: Chen XS]]
-	[[Category: Morimoto, C]]	+	[[Category: Morimoto C]]
-	[[Category: Xiao, X]]	+	[[Category: Xiao X]]
-	[[Category: Yang, H]]	+	[[Category: Yang H]]
-	[[Category: Zirkle, B]]	+	[[Category: Zirkle B]]
-	~~[[Category: Apobec]]~~	+
-	~~[[Category: Deaminase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 12:33, 25 December 2019

OCA — Wed, 25 Dec 2019 12:33:39 GMT

←Older revision		Revision as of 12:33, 25 December 2019
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	==Crystal structure of human APOBEC3B N-terminal Domain==		==Crystal structure of human APOBEC3B N-terminal Domain==
-	<StructureSection load='5tkm' size='340' side='right' caption='[[5tkm]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5tkm' size='340' side='right'caption='[[5tkm]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tkm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tkm]] 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=5TKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TKM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</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='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=5tkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tkm OCA], [http://pdbe.org/5tkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tkm RCSB], [http://www.ebi.ac.uk/pdbsum/5tkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tkm 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=5tkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tkm OCA], [http://pdbe.org/5tkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tkm RCSB], [http://www.ebi.ac.uk/pdbsum/5tkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tkm ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arutiunian, V]]		[[Category: Arutiunian, V]]
	[[Category: Besse, G]]		[[Category: Besse, G]]

OCA at 04:47, 21 September 2017

OCA — Thu, 21 Sep 2017 04:47:03 GMT

←Older revision		Revision as of 04:47, 21 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tkm is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of human APOBEC3B N-terminal Domain==
		+	<StructureSection load='5tkm' size='340' side='right' caption='[[5tkm]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tkm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TKM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=5tkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tkm OCA], [http://pdbe.org/5tkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tkm RCSB], [http://www.ebi.ac.uk/pdbsum/5tkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tkm 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species after RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.

-	~~Authors~~:	+	Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation.,Xiao X, Yang H, Arutiunian V, Fang Y, Besse G, Morimoto C, Zirkle B, Chen XS Nucleic Acids Res. 2017 Jul 7;45(12):7494-7506. doi: 10.1093/nar/gkx362. PMID:28575276<ref>PMID:28575276</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5tkm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arutiunian, V]]
		+	[[Category: Besse, G]]
		+	[[Category: Chen, X S]]
		+	[[Category: Morimoto, C]]
		+	[[Category: Xiao, X]]
		+	[[Category: Yang, H]]
		+	[[Category: Zirkle, B]]
		+	[[Category: Apobec]]
		+	[[Category: Deaminase]]
		+	[[Category: Hydrolase]]

OCA at 17:35, 9 December 2016

OCA — Fri, 09 Dec 2016 17:35:46 GMT

←Older revision		Revision as of 17:35, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 19 Oct 2016 15:58:14 GMT

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

←Older revision

Revision as of 15:58, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tkm is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Oct 2016 15:58:13 GMT

New page: '''Unreleased structure''' The entry 5tkm is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5tkm is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]