+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20031 | |||||||||
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タイトル | Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1) | |||||||||
マップデータ | structure of mouse RAG1/2 PRC complex (DNA1) | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / 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 / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / 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 / endodeoxyribonuclease complex / 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 / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / pre-B cell allelic exclusion / positive regulation of DNA ligation / positive regulation of organ growth / positive regulation of interleukin-1 production / RAGE receptor binding / Regulation of TLR by endogenous ligand / regulation of behavioral fear response / alphav-beta3 integrin-HMGB1 complex / bubble DNA binding / V(D)J遺伝子再構成 / negative regulation of T cell apoptotic process / Apoptosis induced DNA fragmentation / phosphatidylinositol-3,4-bisphosphate binding / inflammatory response to antigenic stimulus / supercoiled DNA binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of thymocyte apoptotic process / MyD88 deficiency (TLR2/4) / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of monocyte chemotaxis / apoptotic cell clearance / dendritic cell chemotaxis / positive regulation of T cell differentiation / DNA binding, bending / 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 / phosphatidylserine binding / B cell lineage commitment / positive regulation of activated T cell proliferation / T cell homeostasis / chemoattractant activity / phosphatidylinositol-3,4,5-trisphosphate binding / DNA topological change / TRAF6 mediated NF-kB activation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Advanced glycosylation endproduct receptor signaling / positive regulation of interleukin-10 production / negative regulation of blood vessel endothelial cell migration / negative regulation of type II interferon production / T cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of blood vessel endothelial cell migration / positive regulation of DNA binding / protein autoubiquitination / Pyroptosis / heterochromatin formation / DNA polymerase binding / positive regulation of autophagy / four-way junction DNA binding / condensed chromosome / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / transcription repressor complex / activation of innate immune response / positive regulation of interleukin-12 production / 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 / RING-type E3 ubiquitin transferase / visual learning / オートファジー / double-strand break repair via nonhomologous end joining / positive regulation of interleukin-6 production / ubiquitin-protein transferase activity / transcription corepressor activity / neuron projection development / ubiquitin protein ligase activity / integrin binding / single-stranded DNA binding / positive regulation of tumor necrosis factor production 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) / Homo sapiens (ヒト) / Escherichia coli K-12 (大腸菌) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.3 Å | |||||||||
データ登録者 | Chen X / Cui Y / Zhou ZH / Yang W / Gellert M | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2020 タイトル: Cutting antiparallel DNA strands in a single active site. 著者: Xuemin Chen / Yanxiang Cui / Robert B Best / Huaibin Wang / Z Hong Zhou / Wei Yang / Martin Gellert / 要旨: A single enzyme active site that catalyzes multiple reactions is a well-established biochemical theme, but how one nuclease site cleaves both DNA strands of a double helix has not been well ...A single enzyme active site that catalyzes multiple reactions is a well-established biochemical theme, but how one nuclease site cleaves both DNA strands of a double helix has not been well understood. In analyzing site-specific DNA cleavage by the mammalian RAG1-RAG2 recombinase, which initiates V(D)J recombination, we find that the active site is reconfigured for the two consecutive reactions and the DNA double helix adopts drastically different structures. For initial nicking of the DNA, a locally unwound and unpaired DNA duplex forms a zipper via alternating interstrand base stacking, rather than melting as generally thought. The second strand cleavage and formation of a hairpin-DNA product requires a global scissor-like movement of protein and DNA, delivering the scissile phosphate into the rearranged active site. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_20031.map.gz | 76.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20031-v30.xml emd-20031.xml | 17.2 KB 17.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_20031.png | 58.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20031 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20031 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_20031.map.gz / 形式: CCP4 / 大きさ: 83.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | structure of mouse RAG1/2 PRC complex (DNA1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : RAG1/2 pre-reaction complex (DNA1)
+超分子 #1: RAG1/2 pre-reaction complex (DNA1)
+分子 #1: V(D)J recombination-activating protein 1
+分子 #2: V(D)J recombination-activating protein 2
+分子 #7: High mobility group protein B1
+分子 #3: DNA (57-MER)
+分子 #4: DNA (46-MER)
+分子 #5: DNA (46-MER)
+分子 #6: DNA (57-MER)
+分子 #8: ZINC ION
+分子 #9: CALCIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.4 |
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グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 42.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期 角度割当 | タイプ: NOT APPLICABLE |
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最終 角度割当 | タイプ: NOT APPLICABLE |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 29224 |