2v87 - Revision history

OCA at 15:09, 13 December 2023

2023-12-13T15:09:27Z

←Older revision		Revision as of 15:09, 13 December 2023
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	<StructureSection load='2v87' size='340' side='right'caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2v87' size='340' side='right'caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V87 FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]~~</~~div~~></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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [https://pdbe.org/2v87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [https://www.ebi.ac.uk/pdbsum/2v87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v87 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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [https://pdbe.org/2v87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [https://www.ebi.ac.uk/pdbsum/2v87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v87 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RAG2_MOUSE RAG2_MOUSE] Core component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. DNA cleavage by the RAG complex occurs in 2 steps: a first nick is introduced in the top strand immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends and 2 blunt, 5'-phosphorylated ends. The chromatin structure plays an essential role in the V(D)J recombination reactions and the presence of histone H3 trimethylated at 'Lys-4' (H3K4me3) stimulates both the nicking and haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA breaks by the RAG complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. In the RAG complex, RAG2 is not the catalytic component but is required for all known catalytic activities mediated by RAG1. It probably acts as a sensor of chromatin state that recruits the RAG complex to H3K4me3.<ref>PMID:2360047</ref> <ref>PMID:8521468</ref> <ref>PMID:9094713</ref> <ref>PMID:16111638</ref> <ref>PMID:19524534</ref> <ref>PMID:19448632</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Ramon-Maiques, S]]	+	[[Category: Ramon-Maiques S]]
-	[[Category: Yang, W]]	+	[[Category: Yang W]]
-	~~[[Category: Covalent modification]]~~	+
-	~~[[Category: Dna recombination]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Histone]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phd finger]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Rag]]~~	+
-	~~[[Category: Recombinase]]~~	+
-	~~[[Category: Symmetric dimethylated arginine]]~~	+
-	~~[[Category: Trimethyl lysine~~]]	+

OCA at 10:42, 7 July 2021

2021-07-07T10:42:45Z

←Older revision		Revision as of 10:42, 7 July 2021
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	<StructureSection load='2v87' size='340' side='right'caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2v87' size='340' side='right'caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2V87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V87 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" id="ligandDat"><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=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</div></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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [~~http~~://pdbe.org/2v87 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2v87 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2v87 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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [https://pdbe.org/2v87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [https://www.ebi.ac.uk/pdbsum/2v87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v87 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 2v87" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2v87" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Recombination-activating gene 3D structures\|Recombination-activating gene 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:09, 10 May 2019

2019-05-10T12:09:49Z

←Older revision		Revision as of 12:09, 10 May 2019
Line 1:		Line 1:

	==Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide==		==Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide==
-	<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2v87' size='340' side='right'caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Ramon-Maiques, S]]		[[Category: Ramon-Maiques, S]]

OCA at 07:49, 6 March 2019

2019-03-06T07:49:25Z

←Older revision		Revision as of 07:49, 6 March 2019
Line 1:		Line 1:

	==Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide==		==Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide==
-	<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>

OCA at 07:41, 12 December 2018

2018-12-12T07:41:15Z

←Older revision		Revision as of 07:41, 12 December 2018
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	<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 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=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/2v87_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/2v87_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Ramon-Maiques, S]]		[[Category: Ramon-Maiques, S]]
	[[Category: Yang, W]]		[[Category: Yang, W]]

OCA at 06:51, 9 March 2017

2017-03-09T06:51:01Z

←Older revision		Revision as of 06:51, 9 March 2017
Line 1:		Line 1:
		+
	==Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide==		==Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide==
	<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 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=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [http://pdbe.org/2v87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [http://www.ebi.ac.uk/pdbsum/2v87 PDBsum]</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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [http://pdbe.org/2v87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [http://www.ebi.ac.uk/pdbsum/2v87 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v87 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Lk3 transgenic mice]]
	[[Category: Ramon-Maiques, S]]		[[Category: Ramon-Maiques, S]]
	[[Category: Yang, W]]		[[Category: Yang, W]]

OCA at 16:24, 9 February 2016

2016-02-09T16:24:03Z

←Older revision		Revision as of 16:24, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 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=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [http://www.ebi.ac.uk/pdbsum/2v87 PDBsum]</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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [http://pdbe.org/2v87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [http://www.ebi.ac.uk/pdbsum/2v87 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2v87 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2v87" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: Ramon-Maiques, S]]		[[Category: Ramon-Maiques, S]]
	[[Category: Yang, W]]		[[Category: Yang, W]]

OCA at 16:18, 19 January 2015

2015-01-19T16:18:17Z

←Older revision		Revision as of 16:18, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [http://www.ebi.ac.uk/pdbsum/2v87 PDBsum]</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=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [http://www.ebi.ac.uk/pdbsum/2v87 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Ramon-Maiques, S.]]	+	[[Category: Ramon-Maiques, S]]
-	[[Category: Yang, W.]]	+	[[Category: Yang, W]]
	[[Category: Covalent modification]]		[[Category: Covalent modification]]
	[[Category: Dna recombination]]		[[Category: Dna recombination]]

OCA at 04:05, 3 October 2014

2014-10-03T04:05:37Z

←Older revision		Revision as of 04:05, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2v87\| PDB=2v87 \| SCENE= }}~~	+	==Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide==
-	===Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide===	+	<StructureSection load='2v87' size='340' side='right' caption='[[2v87]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18025461}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2v87]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V87 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2a23\|2a23]], [[2v83\|2v83]], [[2v85\|2v85]], [[2v86\|2v86]], [[2v88\|2v88]], [[2v89\|2v89]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v87 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v87 RCSB], [http://www.ebi.ac.uk/pdbsum/2v87 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v8/2v87_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Recombination activating gene (RAG) 1 and RAG2 together catalyze V(D)J gene rearrangement in lymphocytes as the first step in the assembly and maturation of antigen receptors. RAG2 contains a plant homeodomain (PHD) near its C terminus (RAG2-PHD) that recognizes histone H3 methylated at lysine 4 (H3K4me) and influences V(D)J recombination. We report here crystal structures of RAG2-PHD alone and complexed with five modified H3 peptides. Two aspects of RAG2-PHD are unique. First, in the absence of the modified peptide, a peptide N-terminal to RAG2-PHD occupies the substrate-binding site, which may reflect an autoregulatory mechanism. Second, in contrast to other H3K4me3-binding PHD domains, RAG2-PHD substitutes a carboxylate that interacts with arginine 2 (R2) with a Tyr, resulting in binding to H3K4me3 that is enhanced rather than inhibited by dimethylation of R2. Five residues involved in histone H3 recognition were found mutated in severe combined immunodeficiency (SCID) patients. Disruption of the RAG2-PHD structure appears to lead to the absence of T and B lymphocytes, whereas failure to bind H3K4me3 is linked to Omenn Syndrome. This work provides a molecular basis for chromatin-dependent gene recombination and presents a single protein domain that simultaneously recognizes two distinct histone modifications, revealing added complexity in the read-out of combinatorial histone modifications.

-	~~==About this Structure==~~	+	The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2.,Ramon-Maiques S, Kuo AJ, Carney D, Matthews AG, Oettinger MA, Gozani O, Yang W Proc Natl Acad Sci U S A. 2007 Nov 27;104(48):18993-8. Epub 2007 Nov 19. PMID:18025461<ref>PMID:18025461</ref>
-	~~[[2v87]] is a~~ 4 ~~chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2V87 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:018025461</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Ramon-Maiques, S.]]		[[Category: Ramon-Maiques, S.]]

OCA at 08:49, 4 September 2013

2013-09-04T08:49:43Z

←Older revision		Revision as of 08:49, 4 September 2013
Line 1:		Line 1:
-	[[Image:2v87.png\|left\|200px]]
-
	{{STRUCTURE_2v87\| PDB=2v87 \| SCENE= }}		{{STRUCTURE_2v87\| PDB=2v87 \| SCENE= }}
-		+	===Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide===
-	===~~CRYSTAL STRUCTURE OF~~ RAG2-PHD ~~FINGER IN COMPLEX WITH H3R2ME2SK4ME3 PEPTIDE~~===	+
-		+
	{{ABSTRACT_PUBMED_18025461}}		{{ABSTRACT_PUBMED_18025461}}

Line 11:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:018025461</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018025461</ref><references group="xtra"/><references/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Ramon-Maiques, S.]]		[[Category: Ramon-Maiques, S.]]