EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Mechanisms of RNF168 nucleosome recognition and ubiquitylation.
ジャーナル・号・ページ	Mol Cell, Vol. 84, Issue 5, Page 839-853.e12, Year 2024
掲載日	2024年3月7日
著者	Qi Hu / Debiao Zhao / Gaofeng Cui / Janarjan Bhandari / James R Thompson / Maria Victoria Botuyan / Georges Mer /
PubMed 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.
リンク	Mol Cell / PubMed:38242129 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.049 - 4.0 Å
構造データ	40604 8smw EMDB-40604, PDB-8smw: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) 手法: EM (単粒子) / 解像度: 3.3 Å 40605 8smx EMDB-40605, PDB-8smx: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) 手法: EM (単粒子) / 解像度: 3.2 Å 40606 8smy EMDB-40606, PDB-8smy: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) 手法: EM (単粒子) / 解像度: 3.2 Å 40607 8smz EMDB-40607, PDB-8smz: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) 手法: EM (単粒子) / 解像度: 3.2 Å 40608 8sn0 EMDB-40608, PDB-8sn0: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) 手法: EM (単粒子) / 解像度: 3.2 Å 40609 8sn1 EMDB-40609, PDB-8sn1: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) 手法: EM (単粒子) / 解像度: 3.3 Å 40610 8sn2 EMDB-40610, PDB-8sn2: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) 手法: EM (単粒子) / 解像度: 3.6 Å 40611 8sn3 EMDB-40611, PDB-8sn3: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) 手法: EM (単粒子) / 解像度: 3.8 Å 40612 8sn4 EMDB-40612, PDB-8sn4: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) 手法: EM (単粒子) / 解像度: 3.7 Å 40613 8sn5 EMDB-40613, PDB-8sn5: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) 手法: EM (単粒子) / 解像度: 3.9 Å 40614 8sn6 EMDB-40614, PDB-8sn6: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) 手法: EM (単粒子) / 解像度: 3.7 Å 40615 8sn7 EMDB-40615, PDB-8sn7: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) 手法: EM (単粒子) / 解像度: 3.7 Å 40616 8sn8 EMDB-40616, PDB-8sn8: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) 手法: EM (単粒子) / 解像度: 3.7 Å 40617 8sn9 EMDB-40617, PDB-8sn9: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) 手法: EM (単粒子) / 解像度: 3.9 Å 40618 8sna EMDB-40618, PDB-8sna: Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) 手法: EM (単粒子) / 解像度: 4.0 Å 41706 8txv EMDB-41706, PDB-8txv: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) 手法: EM (単粒子) / 解像度: 3.8 Å 41707 8txw EMDB-41707, PDB-8txw: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) 手法: EM (単粒子) / 解像度: 3.6 Å 41708 8txx EMDB-41708, PDB-8txx: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) 手法: EM (単粒子) / 解像度: 3.7 Å 41800 8u13 EMDB-41800, PDB-8u13: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) 手法: EM (単粒子) / 解像度: 3.8 Å 41801 8u14 EMDB-41801, PDB-8u14: Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) 手法: EM (単粒子) / 解像度: 3.9 Å 42446 8upf EMDB-42446, PDB-8upf: Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c 手法: EM (単粒子) / 解像度: 3.2 Å PDB-8uq8: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker 手法: X-RAY DIFFRACTION / 解像度: 2.34 Å PDB-8uq9: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker 手法: X-RAY DIFFRACTION / 解像度: 2.3 Å PDB-8uqa: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker 手法: X-RAY DIFFRACTION / 解像度: 2.049 Å PDB-8uqb: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) 手法: X-RAY DIFFRACTION / 解像度: 2.484 Å PDB-8uqc: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) 手法: X-RAY DIFFRACTION / 解像度: 2.61 Å PDB-8uqd: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) 手法: X-RAY DIFFRACTION / 解像度: 3.893 Å PDB-8uqe: Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) 手法: X-RAY DIFFRACTION / 解像度: 3.562 Å
化合物	ChemComp-ZN: Unknown entry ChemComp-CL: Unknown entry / クロリド / 塩化物 ChemComp-GOL: GLYCEROL / グリセロ-ル / グリセリン ChemComp-NA: Unknown entry / ナトリウムカチオン ChemComp-HOH: WATER / 水
由来	homo sapiens (ヒト)
キーワード	STRUCTURAL PROTEIN/DNA/TRANSFERASE (構造) / Nucleosome core particle (ヌクレオソーム) / chromatin (クロマチン) / RNF168 / RING domain / UbcH5c / DNA repair (DNA修復) / DNA double-strand break / Homologous recombination (相同組換え) / 53BP1 / ubiquitin (ユビキチン) / STRUCTURAL PROTEIN-DNA-TRANSFERASE complex (構造) / TRANSFERASE/DNA / TRANSFERASE (転移酵素) / TRANSFERASE-DNA complex / MIU2-LRM domains / BRCA1-BARD1 / Histone H2A (ヒストンH2A) / Histone H2B (ヒストンH2B) / Ubiquitin ligase (ユビキチンリガーゼ) / Ubiquitin-conjugating enzyme (ユビキチン結合酵素) / DNA damage response / DNA double-strand break repair / PROTEIN BINDING (タンパク質) / PROTEIN BINDING-Transferase complex