1rmd: Difference between revisions

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-[[Image:1rmd.gif|left|200px]]<br /><applet load="1rmd" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1rmd, resolution 2.10&Aring;" />
-'''RAG1 DIMERIZATION DOMAIN'''<br />
-==Overview==
+==RAG1 DIMERIZATION DOMAIN==
-The crystal structure of the dimerization domain of the V(D)J recombination-activating protein, RAG1, was solved using zinc anomalous scattering. The structure reveals an unusual combination of multi-class zinc-binding motifs, including a zinc RING finger and a C2H2 zinc finger, that together from a single structural domain. The domain also contains a unique zinc binuclear cluster in place of a normally mononuclear zinc site in the RING finger. Together, four zinc ions help organize the entire domain, including the two helices that form the dimer interface.
+<StructureSection load='1rmd' size='340' side='right'caption='[[1rmd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rmd]] is a 1 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=1RMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RMD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</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'>[https://proteopedia.org/fgij/fg.htm?mol=1rmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmd OCA], [https://pdbe.org/1rmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmd RCSB], [https://www.ebi.ac.uk/pdbsum/1rmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RAG1_MOUSE RAG1_MOUSE] Catalytic 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. In the RAG complex, RAG1 mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all known catalytic activities. DNA cleavage 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 addition to its endonuclease activity, RAG1 also acts as a E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3. Histone H3 monoubiquitination is required for the joining step of V(D)J recombination. Mediates polyubiquitination of KPNA1.<ref>PMID:2598259</ref> <ref>PMID:8521468</ref> <ref>PMID:9094713</ref> <ref>PMID:10601032</ref> <ref>PMID:10678172</ref> <ref>PMID:12629039</ref> <ref>PMID:14671314</ref> <ref>PMID:17028591</ref> <ref>PMID:19524534</ref> <ref>PMID:19118899</ref> <ref>PMID:19448632</ref> <ref>PMID:20122409</ref> <ref>PMID:19396172</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/rm/1rmd_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=1rmd ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-RMD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMD OCA].
+*[[Recombination-activating gene 3D structures|Recombination-activating gene 3D structures]]
+== References ==
-==Reference==
+<references/>
-Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster., Bellon SF, Rodgers KK, Schatz DG, Coleman JE, Steitz TA, Nat Struct Biol. 1997 Jul;4(7):586-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9228952 9228952]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Bellon SF]]
-[[Category: Bellon, S F.]]
+[[Category: Coleman JE]]
-[[Category: Coleman, J E.]]
+[[Category: Rodgers KK]]
-[[Category: Rodgers, K K.]]
+[[Category: Schatz DG]]
-[[Category: Schatz, D G.]]
+[[Category: Steitz TA]]
-[[Category: Steitz, T A.]]
-[[Category: ZN]]
-[[Category: antibody]]
-[[Category: dna-binding protein]]
-[[Category: mad]]
-[[Category: rag1]]
-[[Category: ring finger]]
-[[Category: v(d)j recombination]]
-[[Category: zinc binuclear cluster]]
-[[Category: zinc finger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:52:25 2008''