+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6oeo | ||||||
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タイトル | Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1) | ||||||
要素 |
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キーワード | RECOMBINATION/DNA / V(D)J recombination (V(D)J遺伝子再構成) / DNA Transposition / RAG / SCID / RECOMBINATION (遺伝的組換え) / RECOMBINATION-DNA complex | ||||||
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 / positive regulation of DNA ligation / pre-B cell allelic exclusion / positive regulation of organ growth / positive regulation of interleukin-1 production / Regulation of TLR by endogenous ligand / RAGE receptor binding / 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 / negative regulation of thymocyte apoptotic process / supercoiled DNA binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of monocyte chemotaxis / phosphatidylinositol-3,5-bisphosphate binding / apoptotic cell clearance / dendritic cell chemotaxis / positive regulation of T cell differentiation / IRAK4 deficiency (TLR2/4) / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / regulation of T cell differentiation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / organ growth / T cell lineage commitment / B cell lineage commitment / positive regulation of activated T cell proliferation / phosphatidylserine binding / chemoattractant activity / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / DNA topological change / positive regulation of interleukin-10 production / TRAF6 mediated NF-kB activation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Advanced glycosylation endproduct receptor signaling / 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 / positive regulation of autophagy / heterochromatin formation / DNA polymerase binding / 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 / ubiquitin-protein transferase activity / positive regulation of interleukin-6 production / transcription corepressor activity / neuron projection development / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / 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) Escherichia coli K-12 (大腸菌) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.69 Å | ||||||
データ登録者 | Chen, X. / Cui, Y. / Zhou, Z.H. / 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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6oeo.cif.gz | 473.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6oeo.ent.gz | 358 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6oeo.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/oe/6oeo ftp://data.pdbj.org/pub/pdb/validation_reports/oe/6oeo | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-V(D)J recombination-activating protein ... , 2種, 4分子 ACBD
#1: タンパク質 | 分子量: 119388.352 Da / 分子数: 2 / 変異: E962Q / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Rag1 / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: P15919, 加水分解酵素; エステル加水分解酵素, RING-type E3 ubiquitin transferase #2: タンパク質 | 分子量: 59138.410 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Rag2, Rag-2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P21784 |
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-DNA鎖 , 4種, 4分子 FIGJ
#3: DNA鎖 | 分子量: 15528.942 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli K-12 (大腸菌) |
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#4: DNA鎖 | 分子量: 15275.817 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli K-12 (大腸菌) |
#5: DNA鎖 | 分子量: 18809.023 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli K-12 (大腸菌) |
#6: DNA鎖 | 分子量: 18792.076 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli K-12 (大腸菌) |
-タンパク質 , 1種, 1分子 N
#7: タンパク質 | 分子量: 18897.885 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HMGB1, HMG1 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P09429 |
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-非ポリマー , 2種, 6分子
#8: 化合物 | ChemComp-CA / #9: 化合物 | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: RAG1/2 Nink-forming complex (DNA1) / タイプ: COMPLEX / Entity ID: #1-#7 / 由来: MULTIPLE SOURCES |
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分子量 | 単位: MEGADALTONS / 実験値: YES |
由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: unspecified |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy |
撮影 | 電子線照射量: 42 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.14_3260: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.69 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 109388 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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