+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8sn5 | |||||||||
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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 3) | |||||||||
要素 |
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キーワード | TRANSFERASE/DNA / 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 | 機能・相同性情報 histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / isotype switching / double-strand break repair via classical nonhomologous end joining / 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 / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of protein targeting to mitochondrion / DNA repair-dependent chromatin remodeling / mitochondrion transport along microtubule / fat pad development / response to ionizing radiation / E2 ubiquitin-conjugating enzyme / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / negative regulation of transcription elongation by RNA polymerase II / protein monoubiquitination / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / nucleosome binding / negative regulation of BMP signaling pathway / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein autoubiquitination / protein localization to CENP-A containing chromatin / protein K48-linked ubiquitination / regulation of neuron apoptotic process / Chromatin modifying enzymes / interstrand cross-link repair / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / SUMOylation of DNA damage response and repair proteins / regulation of proteasomal protein catabolic process / Packaging Of Telomere Ends / ubiquitin ligase complex / energy homeostasis / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / Maturation of protein E / ER Quality Control Compartment (ERQC) / nucleosomal DNA binding / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Inhibition of DNA recombination at telomere / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / telomere organization / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / VLDLR internalisation and degradation / Meiotic synapsis / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / positive regulation of DNA repair / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / epigenetic regulation of gene expression / Regulation of pyruvate metabolism / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Downregulation of ERBB2:ERBB3 signaling / Assembly of the ORC complex at the origin of replication / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / SUMOylation of chromatin organization proteins / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
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: 3.9 Å | |||||||||
データ登録者 | Hu, Q. / Botuyan, M.V. / Zhao, D. / Cui, G. / Mer, G. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Mol Cell / 年: 2024 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. | |||||||||
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 | 8sn5.cif.gz | 344.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8sn5.ent.gz | 261.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8sn5.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
文書・要旨 | 8sn5_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8sn5_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 8sn5_validation.xml.gz | 42.9 KB | 表示 | |
CIF形式データ | 8sn5_validation.cif.gz | 67.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sn/8sn5 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/8sn5 | HTTPS FTP |
-関連構造データ
関連構造データ | 40613MC 8smwC 8smxC 8smyC 8smzC 8sn0C 8sn1C 8sn2C 8sn3C 8sn4C 8sn6C 8sn7C 8sn8C 8sn9C 8snaC 8txvC 8txwC 8txxC 8u13C 8u14C 8upfC 8uq8C 8uq9C 8uqaC 8uqbC 8uqcC 8uqdC 8uqeC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
-タンパク質 , 7種, 11分子 AEBFCGDHKLM
#1: タンパク質 | 分子量: 15786.534 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J プラスミド: pHISPP / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P68431 #2: タンパク質 | 分子量: 11743.792 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4 プラスミド: pHISPP / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62805 #3: タンパク質 | 分子量: 13008.156 Da / 分子数: 2 / Mutation: R11S, K15C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P04908 #4: タンパク質 | 分子量: 14084.348 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: H2BC11, H2BFR, HIST1H2BJ / プラスミド: pHISPP / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P06899 #7: タンパク質 | | 分子量: 11903.969 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: RNF168 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8IYW5, RING-type E3 ubiquitin transferase #8: タンパク質 | | 分子量: 17061.418 Da / 分子数: 1 / Mutation: C21I, C107A, C111D, L119K / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2D3, UBC5C, UBCH5C / プラスミド: pHISPP / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: P61077, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme #9: タンパク質 | | 分子量: 9057.391 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: UBB / プラスミド: pHISPP / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG47 |
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-DNA鎖 , 2種, 2分子 IJ
#5: DNA鎖 | 分子量: 45138.770 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) |
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#6: DNA鎖 | 分子量: 45610.043 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) |
-非ポリマー , 1種, 2分子
#10: 化合物 |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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Has protein modification | Y |
-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: Human nucleosome core particle in complex with RNF168 and UbcH5c~Ub タイプ: COMPLEX / Entity ID: #1-#9 / 由来: MULTIPLE SOURCES |
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分子量 | 値: 0.2565 MDa / 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 7.5 |
試料 | 濃度: 0.4 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: 10 mM HEPES, 100 mM NaCl, 1 mM DTT, pH 7.5 |
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: Quantifoil 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 |
-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 FIELD / 倍率(公称値): 130000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 500 nm / Cs: 2.7 mm |
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 | 電子線照射量: 60 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: 14179 詳細: 14179 images were recorded in movie-mode of which 14113 were retained for particle picking. |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 16063830 | ||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 23330 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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