3jbw: Difference between revisions

Line 1:

'''~~Unreleased~~ structure'''

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

== Structural highlights ==

<table><tr><td colspan='2'>[[3jbw]] is a 10 chain structure. 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JBW 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>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jbx|3jbx]], [[3jby|3jby]]</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=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]</span></td></tr>

</table>

== Function ==

[[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).

== Publication Abstract from PubMed ==

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.

~~The entry 3jbw is ON HOLD~~

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>

~~Authors: Ru~~, H.~~, Chambers, M~~.~~G., Fu, T~~.-~~M., Tong, A.B., Liao, M., Wu, H.~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

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

[[Category: ~~Unreleased Structures~~]]

== References ==

[[Category: Fu, T.-M]]

[[Category: ~~Tong~~, ~~A.B~~]]

__TOC__

</StructureSection>

[[Category: Chambers, M G]]

[[Category: Fu, T M]]

[[Category: Liao, M]]

[[Category: Ru, H]]

[[Category: ~~Liao~~, ~~M]]~~

[[Category: Tong, A B]]

~~[[Category: Chambers, M.G~~]]

[[Category: Wu, H]]

[[Category: Antigen receptor gene recombination]]

[[Category: Paired complex]]

[[Category: Rag1]]

[[Category: Rag2]]

[[Category: Recombination-dna complex]]

[[Category: T and b cell development]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+==Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)==
+<StructureSection load='3jbw' size='340' side='right' caption='[[3jbw]], [[Resolution|resolution]] 4.63&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3jbw]] is a 10 chain structure. 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JBW 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>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jbx|3jbx]], [[3jby|3jby]]</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=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]</span></td></tr>
+</table>
+== Function ==
+[[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).
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-The entry 3jbw is ON HOLD
+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>
-Authors: Ru, H., Chambers, M.G., Fu, T.-M., Tong, A.B., Liao, M., Wu, H.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-Description: Cryo-electron microscopy structure of RAG Paired Complex (with NBD, no symmetry)
+<div class="pdbe-citations 3jbw" style="background-color:#fffaf0;"></div>
-[[Category: Unreleased Structures]]
+== References ==
-[[Category: Fu, T.-M]]
+<references/>
-[[Category: Tong, A.B]]
+__TOC__
+</StructureSection>
+[[Category: Chambers, M G]]
+[[Category: Fu, T M]]
+[[Category: Liao, M]]
 [[Category: Ru, H]]
-[[Category: Liao, M]]
+[[Category: Tong, A B]]
-[[Category: Chambers, M.G]]
 [[Category: Wu, H]]
+[[Category: Antigen receptor gene recombination]]
+[[Category: Paired complex]]
+[[Category: Rag1]]
+[[Category: Rag2]]
+[[Category: Recombination-dna complex]]
+[[Category: T and b cell development]]