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Yorodumi- PDB-6cik: Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS comple... -
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-Basic information
Entry | Database: PDB / ID: 6cik | |||||||||
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Title | Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+ | |||||||||
Components |
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Keywords | RECOMBINATION/DNA / VDJ recombination / RSS / RAG1/2 / RECOMBINATION / RECOMBINATION-DNA complex | |||||||||
Function / homology | Function and homology information regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / mature B cell differentiation involved in immune response / T-helper 1 cell activation ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / mature B cell differentiation involved in immune response / T-helper 1 cell activation / C-X-C chemokine binding / T-helper 1 cell differentiation / positive regulation of dendritic cell differentiation / DNA recombinase complex / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of CD4-positive, alpha-beta T cell differentiation / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / neutrophil clearance / pre-B cell allelic exclusion / positive regulation of DNA ligation / positive regulation of interleukin-1 production / RAGE receptor binding / positive regulation of organ growth / Regulation of TLR by endogenous ligand / regulation of behavioral fear response / alphav-beta3 integrin-HMGB1 complex / bubble DNA binding / V(D)J recombination / negative regulation of T cell apoptotic process / Apoptosis induced DNA fragmentation / phosphatidylinositol-3,4-bisphosphate binding / inflammatory response to antigenic stimulus / negative regulation of thymocyte apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / supercoiled DNA binding / phosphatidylinositol-3,5-bisphosphate binding / apoptotic cell clearance / negative regulation of blood vessel endothelial cell migration / dendritic cell chemotaxis / DNA binding, bending / positive regulation of T cell differentiation / positive regulation of vascular endothelial cell proliferation / IRAK4 deficiency (TLR2/4) / regulation of T cell differentiation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / organ growth / condensed chromosome / T cell lineage commitment / positive regulation of DNA binding / B cell lineage commitment / positive regulation of activated T cell proliferation / phosphatidylserine binding / chemoattractant activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / DNA topological change / TRAF6 mediated NF-kB activation / positive regulation of interleukin-10 production / Advanced glycosylation endproduct receptor signaling / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of type II interferon production / T cell differentiation / positive regulation of blood vessel endothelial cell migration / Pyroptosis / protein autoubiquitination / positive regulation of autophagy / DNA polymerase binding / four-way junction DNA binding / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / positive regulation of interleukin-12 production / methylated histone binding / transcription repressor complex / phosphatidylinositol binding / B cell differentiation / thymus development / cytokine activity / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / visual learning / RING-type E3 ubiquitin transferase / heterochromatin formation / autophagy / double-strand break repair via nonhomologous end joining / positive regulation of interleukin-6 production / integrin binding / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / positive regulation of tumor necrosis factor production / neuron projection development / chromatin organization Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å | |||||||||
Authors | Chuenchor, W. / Chen, X. / Kim, M.S. / Gellert, M. / Yang, W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mol Cell / Year: 2018 Title: Cracking the DNA Code for V(D)J Recombination. Authors: Min-Sung Kim / Watchalee Chuenchor / Xuemin Chen / Yanxiang Cui / Xing Zhang / Z Hong Zhou / Martin Gellert / Wei Yang / Abstract: To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have ...To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cik.cif.gz | 499.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cik.ent.gz | 384.2 KB | Display | PDB format |
PDBx/mmJSON format | 6cik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cik_validation.pdf.gz | 518.5 KB | Display | wwPDB validaton report |
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Full document | 6cik_full_validation.pdf.gz | 553.1 KB | Display | |
Data in XML | 6cik_validation.xml.gz | 71.5 KB | Display | |
Data in CIF | 6cik_validation.cif.gz | 99 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/6cik ftp://data.pdbj.org/pub/pdb/validation_reports/ci/6cik | HTTPS FTP |
-Related structure data
Related structure data | 7470C 7480C 5zdzC 5ze0C 5ze1C 5ze2C 6cg0C 6cijC 6cilC 6cimC 4wwxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
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-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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