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基本情報
登録情報 | データベース: PDB / ID: 7l9p | ||||||
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タイトル | Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex | ||||||
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![]() | NUCLEAR PROTEIN / REV7 / SHLD2 / SHLD3 / TRIP13 | ||||||
機能・相同性 | ![]() somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / meiotic recombination checkpoint signaling / zeta DNA polymerase complex / synaptonemal complex assembly / telomere maintenance in response to DNA damage / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / meiotic recombination checkpoint signaling / zeta DNA polymerase complex / synaptonemal complex assembly / telomere maintenance in response to DNA damage / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / reciprocal meiotic recombination / female meiosis I / oocyte maturation / negative regulation of ubiquitin protein ligase activity / regulation of double-strand break repair via homologous recombination / oogenesis / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair via nonhomologous end joining / male meiosis I / spermatid development / negative regulation of double-strand break repair via homologous recombination / male germ cell nucleus / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / transcription coregulator activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / negative regulation of protein catabolic process / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / spindle / chromosome / positive regulation of peptidyl-serine phosphorylation / double-strand break repair / actin cytoskeleton / site of double-strand break / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell division / DNA repair / positive regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
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: 3.6 Å | ||||||
![]() | Xie, W. / Patel, D.J. | ||||||
![]() | ![]() タイトル: Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex. 著者: Wei Xie / Shengliu Wang / Juncheng Wang / M Jason de la Cruz / Guotai Xu / Maurizio Scaltriti / Dinshaw J Patel / ![]() 要旨: The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA ATPase TRIP13 remodels Shieldin to regulate DNA ...The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA ATPase TRIP13 remodels Shieldin to regulate DNA repair pathway choice. Here we report crystal structures of human SHLD3-REV7 binary and fused SHLD2-SHLD3-REV7 ternary complexes, revealing that assembly of Shieldin requires fused SHLD2-SHLD3 induced conformational heterodimerization of open (O-REV7) and closed (C-REV7) forms of REV7. We also report the cryogenic electron microscopy (cryo-EM) structures of the ATPγS-bound fused SHLD2-SHLD3-REV7-TRIP13 complexes, uncovering the principles underlying the TRIP13-mediated disassembly mechanism of the Shieldin complex. We demonstrate that the N terminus of REV7 inserts into the central channel of TRIP13, setting the stage for pulling the unfolded N-terminal peptide of C-REV7 through the central TRIP13 hexameric channel. The primary interface involves contacts between the safety-belt segment of C-REV7 and a conserved and negatively charged loop of TRIP13. This process is mediated by ATP hydrolysis-triggered rotatory motions of the TRIP13 ATPase, thereby resulting in the disassembly of the Shieldin complex. | ||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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-検証レポート
文書・要旨 | ![]() | 1.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.4 MB | 表示 | |
XML形式データ | ![]() | 88.1 KB | 表示 | |
CIF形式データ | ![]() | 130.8 KB | 表示 | |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 48562.547 Da / 分子数: 6 / 変異: E253Q / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 24323.348 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: closed form / 由来: (組換発現) ![]() ![]() ![]() #3: タンパク質 | 分子量: 10678.139 Da / 分子数: 2 Fragment: SHLD2 (UNP residues 5-19) + linker + SHLD3 (UNP residues 2-58) 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #4: 化合物 | ChemComp-AGS / 研究の焦点であるリガンドがあるか | Y | |
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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 |
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試料調製
構成要素 | 名称: SHLD2.3-REV7(4)-TRIP13(E253Q) complex with ATP-gamma-S タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT |
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由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
緩衝液 | pH: 7.3 詳細: 20 mM HEPES, pH 7.3, 300 mM NaCl, 5 mM MgCl2, 0.1 mM ATP-gamma-S, 1 mM DTT |
試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: GOLD / グリッドのタイプ: UltrAuFoil R1.2/1.3 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K / 詳細: 1.5-second blot, blot force of 0 |
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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: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): -2500 nm / 最小 デフォーカス(公称値): -1000 nm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 0.075 sec. / 電子線照射量: 53 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 40 |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.18_3855: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 104023 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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