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基本情報
登録情報 | ![]() | |||||||||
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タイトル | Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) | |||||||||
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![]() | Nucleosome core particle / chromatin / RNF168 / RING domain / UbcH5c / DNA repair / DNA double-strand break / Homologous recombination / 53BP1 / ubiquitin / STRUCTURAL PROTEIN-DNA-TRANSFERASE complex / TRANSFERASE / TRANSFERASE-DNA complex | |||||||||
機能・相同性 | ![]() histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / double-strand break repair via classical nonhomologous end joining / isotype switching / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / double-strand break repair via classical nonhomologous end joining / isotype switching / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / DNA repair-dependent chromatin remodeling / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / positive regulation of protein targeting to mitochondrion / fat pad development / K63-linked polyubiquitin modification-dependent protein binding / E2 ubiquitin-conjugating enzyme / response to ionizing radiation / female gonad development / seminiferous tubule development / male meiosis I / negative regulation of transcription elongation by RNA polymerase II / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / negative regulation of BMP signaling pathway / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / heterochromatin organization / protein localization to CENP-A containing chromatin / protein autoubiquitination / protein K48-linked ubiquitination / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / interstrand cross-link repair / SUMOylation of DNA damage response and repair proteins / energy homeostasis / epigenetic regulation of gene expression / regulation of neuron apoptotic process / Packaging Of Telomere Ends / nucleosomal DNA binding / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / nucleosome binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Maturation of protein E / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Inhibition of DNA recombination at telomere / Meiotic synapsis / p75NTR recruits signalling complexes / positive regulation of DNA repair / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / telomere organization / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / RNA Polymerase I Promoter Opening / NF-kB is activated and signals survival / Interleukin-7 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.7 Å | |||||||||
![]() | Hu Q / Botuyan MV / Zhao D / Cui G / Mer G | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. 著者: Qi Hu / Debiao Zhao / Gaofeng Cui / Janarjan Bhandari / James R Thompson / Maria Victoria Botuyan / Georges Mer / ![]() 要旨: RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for ...RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation. | |||||||||
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構造の表示
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マップデータ | ![]() | 38.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 27.9 KB 27.9 KB | 表示 表示 | ![]() |
画像 | ![]() | 108.5 KB | ||
マスクデータ | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.7 KB | ||
その他 | ![]() ![]() | 50.1 MB 50.1 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 910.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 910.5 KB | 表示 | |
XML形式データ | ![]() | 12 KB | 表示 | |
CIF形式データ | ![]() | 14 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 8sn7MC ![]() 8smwC ![]() 8smxC ![]() 8smyC ![]() 8smzC ![]() 8sn0C ![]() 8sn1C ![]() 8sn2C ![]() 8sn3C ![]() 8sn4C ![]() 8sn5C ![]() 8sn6C ![]() 8sn8C ![]() 8sn9C ![]() 8snaC ![]() 8txvC ![]() 8txwC ![]() 8txxC ![]() 8u13C ![]() 8u14C ![]() 8upfC ![]() 8uq8C ![]() 8uq9C ![]() 8uqaC ![]() 8uqbC ![]() 8uqcC ![]() 8uqdC ![]() 8uqeC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.328 Å | ||||||||||||||||||||
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_40615_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_40615_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Human nucleosome core particle in complex with RNF168 and UbcH5c~Ub
+超分子 #1: Human nucleosome core particle in complex with RNF168 and UbcH5c~Ub
+分子 #1: Histone H3.1
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1-B/E
+分子 #4: Histone H2B type 1-J
+分子 #7: E3 ubiquitin-protein ligase RNF168
+分子 #8: Ubiquitin-conjugating enzyme E2 D3
+分子 #9: Polyubiquitin-B
+分子 #5: DNA (147-MER)
+分子 #6: DNA (147-MER)
+分子 #10: ZINC 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.4 mg/mL |
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緩衝液 | pH: 7.5 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
詳細 | 10 mM HEPES, 100 mM NaCl, 1 mM DTT, pH 7.5 |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | 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: 14179 / 平均電子線量: 60.0 e/Å2 詳細: 14179 images were recorded in movie-mode of which 14113 were retained for particle picking. |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 130000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
初期モデル |
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精密化 | 空間: REAL / プロトコル: RIGID BODY FIT | ||||||||||
得られたモデル | ![]() PDB-8sn7: |