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-基本情報
登録情報 | データベース: PDB / ID: 6cil | |||||||||
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タイトル | PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+ | |||||||||
要素 |
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キーワード | RECOMBINATION/DNA / VDJ recombination / RSS / RAG1/2 / RECOMBINATION / RECOMBINATION-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 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 / 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 / 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 / negative regulation of blood vessel endothelial cell migration / 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 / condensed chromosome / 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 / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / positive regulation of tumor necrosis factor production / neuron projection development / integrin binding / chromatin organization 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 4.15 Å | |||||||||
データ登録者 | Chuenchor, W. / Chen, X. / Kim, M.S. / Gellert, M. / Yang, W. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Mol Cell / 年: 2018 タイトル: Cracking the DNA Code for V(D)J Recombination. 著者: Min-Sung Kim / Watchalee Chuenchor / Xuemin Chen / Yanxiang Cui / Xing Zhang / Z Hong Zhou / Martin Gellert / Wei Yang / 要旨: 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. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6cil.cif.gz | 486.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6cil.ent.gz | 375.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6cil.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ci/6cil ftp://data.pdbj.org/pub/pdb/validation_reports/ci/6cil | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
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非結晶学的対称性 (NCS) | NCSドメイン:
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