2v83: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2v83.png|left|200px]]
-<!--
+==Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide==
-The line below this paragraph, containing "STRUCTURE_2v83", creates the "Structure Box" on the page.
+<StructureSection load='2v83' size='340' side='right'caption='[[2v83]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2v83]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V83 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V83 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2v83|  PDB=2v83  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v83 OCA], [https://pdbe.org/2v83 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v83 RCSB], [https://www.ebi.ac.uk/pdbsum/2v83 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v83 ProSAT]</span></td></tr>
+</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 ==
+[[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/v8/2v83_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/main_output.php?pdb_ID=2v83 ConSurf].
+<div style="clear:both"></div>
-===CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3K4ME3 PEPTIDE===
+==See Also==
+*[[Recombination-activating gene 3D structures|Recombination-activating gene 3D structures]]
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_18025461}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 18025461 is the PubMed ID number.
+</StructureSection>
--->
+[[Category: Homo sapiens]]
-{{ABSTRACT_PUBMED_18025461}}
+[[Category: Large Structures]]
-==About this Structure==
-V83 is a [[Single protein]] structure of 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=2V83 OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/18025461 18025461]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[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: Trimetyl lysine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 17:37:25 2008''