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基本情報
登録情報 | データベース: PDB / ID: 6ftx | ||||||
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タイトル | Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome | ||||||
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![]() | MOTOR PROTEIN / Chromatin remodellers | ||||||
機能・相同性 | ![]() nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / SLIK (SAGA-like) complex / rDNA binding / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / hypothalamus gonadotrophin-releasing hormone neuron development ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / SLIK (SAGA-like) complex / rDNA binding / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / hypothalamus gonadotrophin-releasing hormone neuron development / SAGA complex / female meiosis I / sister chromatid cohesion / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / termination of RNA polymerase II transcription / female gonad development / seminiferous tubule development / termination of RNA polymerase I transcription / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ATP-dependent activity, acting on DNA / : / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / neuron projection morphogenesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Translesion synthesis by POLI / positive regulation of protein ubiquitination / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / helicase activity / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() synthetic construct (人工物) | ||||||
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: 4.5 Å | ||||||
![]() | Sundaramoorthy, R. / Owen-hughes, T. / Norman, D.G. / Hughes, A. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. 著者: Ramasubramanian Sundaramoorthy / Amanda L Hughes / Hassane El-Mkami / David G Norman / Helder Ferreira / Tom Owen-Hughes / ![]() 要旨: ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the ...ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented. | ||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 545.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 420.5 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 945.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 98.4 KB | 表示 | |
CIF形式データ | ![]() | 144.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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
-タンパク質 , 7種, 11分子 ABFCGDHENOW
#1: タンパク質 | 分子量: 11431.358 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() | ||||||||||
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#2: タンパク質 | 分子量: 11394.426 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 発現宿主: ![]() ![]() #3: タンパク質 | 分子量: 14093.436 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 発現宿主: ![]() ![]() #4: タンパク質 | 分子量: 13939.228 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 遺伝子: LOC108648866 / 発現宿主: ![]() ![]() #5: タンパク質 | | 分子量: 12329.330 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 遺伝子: h3f3c / 発現宿主: ![]() ![]() #8: タンパク質 | 分子量: 8576.831 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #9: タンパク質 | | 分子量: 102152.859 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: CHD1, SCKG_4184 / 発現宿主: ![]() ![]() |
-DNA鎖 , 2種, 2分子 IJ
#6: DNA鎖 | 分子量: 48792.086 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
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#7: DNA鎖 | 分子量: 49678.613 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-非ポリマー , 2種, 2分子 


#10: 化合物 | ChemComp-BEF / |
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#11: 化合物 | ChemComp-ADP / |
-詳細
Has protein modification | 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 |
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分子量 | 値: 0.450 MDa / 実験値: NO | ||||||||||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 | ||||||||||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: Sample was gel filtration purified and it is monodisperse | ||||||||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: C-flat-1.2/1.3 4C | ||||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
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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 / 倍率(公称値): 35714 X / 倍率(補正後): 35714 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 1500 nm / Calibrated defocus min: 1500 nm / 最大 デフォーカス(補正後): 4000 nm / Cs: 2.7 mm / C2レンズ絞り径: 70 µm / アライメント法: BASIC |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER 最高温度: 170 K / 最低温度: 170 K |
撮影 | 平均露光時間: 0.32 sec. / 電子線照射量: 1.25 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 撮影したグリッド数: 1 / 実像数: 1300 |
電子光学装置 | エネルギーフィルター名称: GIF Quantum LS |
画像スキャン | サンプリングサイズ: 5 µm / 横: 3870 / 縦: 3870 / 動画フレーム数/画像: 32 / 利用したフレーム数/画像: 5-28 |
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解析
ソフトウェア | 名称: REFMAC / バージョン: 5.8.0230 / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 860000 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 135000 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 204 / プロトコル: FLEXIBLE FIT / 空間: RECIPROCAL / Target criteria: Cross-correlation coefficient | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | Cor.coef. Fo:Fc: 0.304 / 最高解像度: 4.5 Å / % reflection obs: 100 % / SU B: 200.492 / SU ML: 0.762 / ESU R: 0.624 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 溶媒モデル: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 266.837 Å2
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精密化ステップ | サイクル: 1 / 合計: 21021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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