OCA at 07:22, 14 February 2024

OCA — Wed, 14 Feb 2024 07:22:05 GMT

←Older revision		Revision as of 07:22, 14 February 2024
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8t4r is ~~ON HOLD until Paper Publication~~	+	==RAG2-PHD finger in complex with H3K4tBuNle peptide==
-		+	<StructureSection load='8t4r' size='340' side='right'caption='[[8t4r]], [[Resolution\|resolution]] 1.20Å' scene=''>
-	~~Authors~~: ~~Kean~~, K.M., ~~Travis~~, C.R., ~~Waters~~, M.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[8t4r]] 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=8T4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8T4R FirstGlance]. <br>
-	~~Description~~: ~~RAG2~~-~~PHD finger~~ in complex ~~with H3K4tBuNle peptide~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.2Å</td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4WQ:(2S)-2-AMINO-7,7-DIMETHYLOCTANOIC+ACID'>4WQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: Kean~~, K.M~~]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8t4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8t4r OCA], [https://pdbe.org/8t4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8t4r RCSB], [https://www.ebi.ac.uk/pdbsum/8t4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8t4r ProSAT]</span></td></tr>
-	[[Category: ~~Waters, M.L~~]]	+	</table>
-	[[Category: ~~Travis, C.R~~]]	+	== Disease ==
		+	[https://www.uniprot.org/uniprot/RAG2_HUMAN RAG2_HUMAN] Severe combined immunodeficiency due to complete RAG1/2 deficiency;Omenn syndrome;Combined immunodeficiency with granulomatosis. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry.
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RAG2_HUMAN RAG2_HUMAN] 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 (By similarity).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Kean KM]]
		+	[[Category: Travis CR]]
		+	[[Category: Waters ML]]

OCA at 11:08, 26 July 2023

OCA — Wed, 26 Jul 2023 11:08:19 GMT

←Older revision		Revision as of 11:08, 26 July 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8t4r is ON HOLD	+	The entry 8t4r is ON HOLD until Paper Publication

	Authors: Kean, K.M., Travis, C.R., Waters, M.L.		Authors: Kean, K.M., Travis, C.R., Waters, M.L.

OCA: Protected "8t4r" [edit=sysop:move=sysop]

OCA — Wed, 21 Jun 2023 08:31:06 GMT

Protected "8t4r" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:31, 21 June 2023

OCA: New page: '''Unreleased structure''' The entry 8t4r is ON HOLD Authors: Kean, K.M., Travis, C.R., Waters, M.L. Description: RAG2-PHD finger in complex with H3K4tBuNle peptide [[Category: Unrelea...

OCA — Wed, 21 Jun 2023 08:31:05 GMT

New page: '''Unreleased structure''' The entry 8t4r is ON HOLD Authors: Kean, K.M., Travis, C.R., Waters, M.L. Description: RAG2-PHD finger in complex with H3K4tBuNle peptide [[Category: Unrelea...

New page

'''Unreleased structure'''

The entry 8t4r is ON HOLD

Authors: Kean, K.M., Travis, C.R., Waters, M.L.

Description: RAG2-PHD finger in complex with H3K4tBuNle peptide
[[Category: Unreleased Structures]]
[[Category: Kean, K.M]]
[[Category: Waters, M.L]]
[[Category: Travis, C.R]]

8t4r - Revision history

OCA at 07:22, 14 February 2024

OCA at 11:08, 26 July 2023

OCA: Protected "8t4r" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8t4r is ON HOLD Authors: Kean, K.M., Travis, C.R., Waters, M.L. Description: RAG2-PHD finger in complex with H3K4tBuNle peptide [[Category: Unrelea...