6e94 - Revision history

OCA at 14:40, 13 March 2024

OCA — Wed, 13 Mar 2024 14:40:06 GMT

←Older revision		Revision as of 14:40, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6e94' size='340' side='right'caption='[[6e94]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='6e94' size='340' side='right'caption='[[6e94]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e94]] is a 3 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=6E94 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6E94 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e94]] is a 3 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=6E94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E94 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]] 1.594Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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">ZBTB38 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=6e94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e94 OCA], [https://pdbe.org/6e94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e94 RCSB], [https://www.ebi.ac.uk/pdbsum/6e94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e94 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=6e94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e94 OCA], [~~http~~://pdbe.org/6e94 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6e94 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6e94 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6e94 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ZBT38_HUMAN ZBT38_HUMAN]] Transcriptional regulator with bimodal DNA-binding specificity. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to E-box elements (5'-CACGTG-3'). Can also bind specifically to a single methyl-CpG pair. Represses transcription in a methyl-CpG-dependent manner (PubMed:16354688). Plays an important role in regulating DNA replication and common fragile sites (CFS) stability in a RBBP6- and MCM10-dependent manner; represses expression of MCM10 which plays an important role in DNA-replication (PubMed:24726359). Acts as a transcriptional activator. May be involved in the differentiation and/or survival of late postmitotic neurons (By similarity).[UniProtKB:Q5EXX3]<ref>PMID:16354688</ref> <ref>PMID:24726359</ref>	+	[https://www.uniprot.org/uniprot/ZBT38_HUMAN ZBT38_HUMAN] Transcriptional regulator with bimodal DNA-binding specificity. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to E-box elements (5'-CACGTG-3'). Can also bind specifically to a single methyl-CpG pair. Represses transcription in a methyl-CpG-dependent manner (PubMed:16354688). Plays an important role in regulating DNA replication and common fragile sites (CFS) stability in a RBBP6- and MCM10-dependent manner; represses expression of MCM10 which plays an important role in DNA-replication (PubMed:24726359). Acts as a transcriptional activator. May be involved in the differentiation and/or survival of late postmitotic neurons (By similarity).[UniProtKB:Q5EXX3]<ref>PMID:16354688</ref> <ref>PMID:24726359</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Methyl-CpG binding proteins (MBPs) are selective readers of DNA methylation that play an essential role in mediating cellular transcription processes in both normal and diseased cells. This physiological function of MBPs has generated significant interest in understanding the mechanisms by which these proteins read and interpret DNA methylation signals. Zinc finger and BTB domain-containing 38 (ZBTB38) represents one member of the zinc finger (ZF) family of MBPs. We recently demonstrated that the C-terminal ZFs of ZBTB38 exhibit methyl-selective DNA binding within the ((A/G)TmCG(G/A)(mC/T)(G/A)) context both in vitro and within cells. Here we report the crystal structure of the first four C-terminal ZBTB38 ZFs (ZFs 6-9) in complex with the previously identified methylated consensus sequence at 1.75 A resolution. From the structure, methyl-selective binding is preferentially localized at the 5'-mCpG site of the bound DNA which is facilitated through a series of base-specific interactions from residues within the alpha-helices of ZF7 and ZF8. ZF6 and ZF9 primarily stabilize ZF7 and ZF8 to facilitate the core base-specific interactions. Further structural and biochemical analyses, including solution NMR spectroscopy and electrophoretic mobility gel shift assays, revealed that the C-terminal ZFs of ZBTB38 utilize an alternative mode of mCpG recognition from the ZF MBPs structurally evaluated to date. Combined these findings provide insight into the mechanism by which this ZF domain of ZBTB38 selectively recognizes methylated CpG sites and expands our understanding for how ZF-containing proteins can interpret this essential epigenetic mark.	+
-		+
-	Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.,Hudson NO, Whitby FG, Buck-Koehntop BA J Biol Chem. 2018 Oct 24. pii: RA118.005147. doi: 10.1074/jbc.RA118.005147. PMID:30355731<ref>PMID:30355731</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6e94" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Buck-Koehntop~~, B A~~]]	+	[[Category: Buck-Koehntop BA]]
-	[[Category: Hudson~~, N O~~]]	+	[[Category: Hudson NO]]
-	[[Category: Whitby~~, F G]]~~	+	[[Category: Whitby FG]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Zbtb38 methylated dna zinc finger~~]]	+

OCA at 08:39, 27 November 2019

OCA — Wed, 27 Nov 2019 08:39:25 GMT

←Older revision		Revision as of 08:39, 27 November 2019
Line 1:		Line 1:

	==Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in complex with methylated DNA==		==Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in complex with methylated DNA==
-	<StructureSection load='6e94' size='340' side='right' caption='[[6e94]], [[Resolution\|resolution]] 1.59Å' scene=''>	+	<StructureSection load='6e94' size='340' side='right'caption='[[6e94]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6e94]] is a 3 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=6E94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E94 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6e94]] is a 3 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=6E94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E94 FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Buck-Koehntop, B A]]		[[Category: Buck-Koehntop, B A]]
	[[Category: Hudson, N O]]		[[Category: Hudson, N O]]

OCA at 06:20, 2 January 2019

OCA — Wed, 02 Jan 2019 06:20:26 GMT

←Older revision		Revision as of 06:20, 2 January 2019
Line 3:		Line 3:
	<StructureSection load='6e94' size='340' side='right' caption='[[6e94]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='6e94' size='340' side='right' caption='[[6e94]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e94]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E94 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e94]] is a 3 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=6E94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E94 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ZBTB38 ([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=6e94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e94 OCA], [http://pdbe.org/6e94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e94 RCSB], [http://www.ebi.ac.uk/pdbsum/6e94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e94 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=6e94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e94 OCA], [http://pdbe.org/6e94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e94 RCSB], [http://www.ebi.ac.uk/pdbsum/6e94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e94 ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Buck-Koehntop, B A]]		[[Category: Buck-Koehntop, B A]]
	[[Category: Hudson, N O]]		[[Category: Hudson, N O]]

OCA at 12:15, 7 November 2018

OCA — Wed, 07 Nov 2018 12:15:04 GMT

←Older revision		Revision as of 12:15, 7 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6e94 is ~~ON HOLD~~	+	==Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in complex with methylated DNA==
		+	<StructureSection load='6e94' size='340' side='right' caption='[[6e94]], [[Resolution\|resolution]] 1.59Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6e94]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E94 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E94 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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=6e94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e94 OCA], [http://pdbe.org/6e94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e94 RCSB], [http://www.ebi.ac.uk/pdbsum/6e94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e94 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ZBT38_HUMAN ZBT38_HUMAN]] Transcriptional regulator with bimodal DNA-binding specificity. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to E-box elements (5'-CACGTG-3'). Can also bind specifically to a single methyl-CpG pair. Represses transcription in a methyl-CpG-dependent manner (PubMed:16354688). Plays an important role in regulating DNA replication and common fragile sites (CFS) stability in a RBBP6- and MCM10-dependent manner; represses expression of MCM10 which plays an important role in DNA-replication (PubMed:24726359). Acts as a transcriptional activator. May be involved in the differentiation and/or survival of late postmitotic neurons (By similarity).[UniProtKB:Q5EXX3]<ref>PMID:16354688</ref> <ref>PMID:24726359</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methyl-CpG binding proteins (MBPs) are selective readers of DNA methylation that play an essential role in mediating cellular transcription processes in both normal and diseased cells. This physiological function of MBPs has generated significant interest in understanding the mechanisms by which these proteins read and interpret DNA methylation signals. Zinc finger and BTB domain-containing 38 (ZBTB38) represents one member of the zinc finger (ZF) family of MBPs. We recently demonstrated that the C-terminal ZFs of ZBTB38 exhibit methyl-selective DNA binding within the ((A/G)TmCG(G/A)(mC/T)(G/A)) context both in vitro and within cells. Here we report the crystal structure of the first four C-terminal ZBTB38 ZFs (ZFs 6-9) in complex with the previously identified methylated consensus sequence at 1.75 A resolution. From the structure, methyl-selective binding is preferentially localized at the 5'-mCpG site of the bound DNA which is facilitated through a series of base-specific interactions from residues within the alpha-helices of ZF7 and ZF8. ZF6 and ZF9 primarily stabilize ZF7 and ZF8 to facilitate the core base-specific interactions. Further structural and biochemical analyses, including solution NMR spectroscopy and electrophoretic mobility gel shift assays, revealed that the C-terminal ZFs of ZBTB38 utilize an alternative mode of mCpG recognition from the ZF MBPs structurally evaluated to date. Combined these findings provide insight into the mechanism by which this ZF domain of ZBTB38 selectively recognizes methylated CpG sites and expands our understanding for how ZF-containing proteins can interpret this essential epigenetic mark.

-	~~Authors: Hudson, N.O~~., Whitby~~, F.G.~~, Buck-Koehntop~~, B~~.A.	+	Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.,Hudson NO, Whitby FG, Buck-Koehntop BA J Biol Chem. 2018 Oct 24. pii: RA118.005147. doi: 10.1074/jbc.RA118.005147. PMID:30355731<ref>PMID:30355731</ref>

-	~~Description: Crystal Structure~~ of ~~ZBTB38 C~~-~~terminal Zinc Fingers 6~~-~~9 K1055R in complex with methylated DNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Hudson, N.O]]	+	<div class="pdbe-citations 6e94" style="background-color:#fffaf0;"></div>
-	[[Category: Whitby, F.G]]	+	== References ==
-	[[Category: ~~Buck~~-~~Koehntop, B.A~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Buck-Koehntop, B A]]
		+	[[Category: Hudson, N O]]
		+	[[Category: Whitby, F G]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Zbtb38 methylated dna zinc finger]]

OCA at 04:40, 22 August 2018

OCA — Wed, 22 Aug 2018 04:40:47 GMT

←Older revision		Revision as of 04:40, 22 August 2018
Line 5:		Line 5:
	Authors: Hudson, N.O., Whitby, F.G., Buck-Koehntop, B.A.		Authors: Hudson, N.O., Whitby, F.G., Buck-Koehntop, B.A.

-	Description: Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R ~~domain~~ in complex with ~~the~~ methylated DNA ~~binding motif~~	+	Description: Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in complex with methylated DNA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hudson, N.O]]		[[Category: Hudson, N.O]]
	[[Category: Whitby, F.G]]		[[Category: Whitby, F.G]]
	[[Category: Buck-Koehntop, B.A]]		[[Category: Buck-Koehntop, B.A]]

OCA: Protected "6e94" [edit=sysop:move=sysop]

OCA — Thu, 09 Aug 2018 19:55:43 GMT

Protected "6e94" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:55, 9 August 2018

OCA: New page: '''Unreleased structure''' The entry 6e94 is ON HOLD Authors: Hudson, N.O., Whitby, F.G., Buck-Koehntop, B.A. Description: Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055...

OCA — Thu, 09 Aug 2018 19:55:42 GMT

New page: '''Unreleased structure''' The entry 6e94 is ON HOLD Authors: Hudson, N.O., Whitby, F.G., Buck-Koehntop, B.A. Description: Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055...

New page

'''Unreleased structure'''

The entry 6e94 is ON HOLD

Authors: Hudson, N.O., Whitby, F.G., Buck-Koehntop, B.A.

Description: Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R domain in complex with the methylated DNA binding motif
[[Category: Unreleased Structures]]
[[Category: Hudson, N.O]]
[[Category: Whitby, F.G]]
[[Category: Buck-Koehntop, B.A]]