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3jbw

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<SX load='3jbw' size='340' side='right' viewer='molstar' caption='[[3jbw]], [[Resolution|resolution]] 4.63&Aring;' scene=''>
<SX load='3jbw' size='340' side='right' viewer='molstar' caption='[[3jbw]], [[Resolution|resolution]] 4.63&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3jbw]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3JBW FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3jbw]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JBW FirstGlance]. <br>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.631&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jbx|3jbx]], [[3jby|3jby]]</td></tr>
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<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>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rag1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio]), rag2, rag-2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3jbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbw OCA], [https://pdbe.org/3jbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jbw RCSB], [https://www.ebi.ac.uk/pdbsum/3jbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbw ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3jbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jbw OCA], [http://pdbe.org/3jbw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jbw RCSB], [http://www.ebi.ac.uk/pdbsum/3jbw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3jbw ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/RAG1_DANRE RAG1_DANRE]] 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. 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 (By similarity).
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[https://www.uniprot.org/uniprot/RAG2_DANRE RAG2_DANRE] 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. 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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Diverse repertoires of antigen-receptor genes that result from combinatorial splicing of coding segments by V(D)J recombination are hallmarks of vertebrate immunity. The (RAG1-RAG2)2 recombinase (RAG) recognizes recombination signal sequences (RSSs) containing a heptamer, a spacer of 12 or 23 base pairs, and a nonamer (12-RSS or 23-RSS) and introduces precise breaks at RSS-coding segment junctions. RAG forms synaptic complexes only with one 12-RSS and one 23-RSS, a dogma known as the 12/23 rule that governs the recombination fidelity. We report cryo-electron microscopy structures of synaptic RAG complexes at up to 3.4 A resolution, which reveal a closed conformation with base flipping and base-specific recognition of RSSs. Distortion at RSS-coding segment junctions and base flipping in coding segments uncover the two-metal-ion catalytic mechanism. Induced asymmetry involving tilting of the nonamer-binding domain dimer of RAG1 upon binding of HMGB1-bent 12-RSS or 23-RSS underlies the molecular mechanism for the 12/23 rule.
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Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.,Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H Cell. 2015 Nov 19;163(5):1138-52. doi: 10.1016/j.cell.2015.10.055. Epub 2015 Nov , 5. PMID:26548953<ref>PMID:26548953</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3jbw" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Recombination-activating gene|Recombination-activating gene]]
*[[Recombination-activating gene|Recombination-activating gene]]
*[[Recombination-activating gene 3D structures|Recombination-activating gene 3D structures]]
*[[Recombination-activating gene 3D structures|Recombination-activating gene 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</SX>
</SX>
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[[Category: Brachidanio rerio]]
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[[Category: Danio rerio]]
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[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Chambers, M G]]
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[[Category: Chambers MG]]
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[[Category: Fu, T M]]
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[[Category: Fu T-M]]
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[[Category: Liao, M]]
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[[Category: Liao M]]
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[[Category: Ru, H]]
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[[Category: Ru H]]
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[[Category: Tong, A B]]
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[[Category: Tong AB]]
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[[Category: Wu, H]]
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[[Category: Wu H]]
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[[Category: Antigen receptor gene recombination]]
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[[Category: Paired complex]]
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[[Category: Rag1]]
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[[Category: Rag2]]
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[[Category: Recombination-dna complex]]
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[[Category: T and b cell development]]
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Current revision

Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)

3jbw, resolution 4.63Å

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