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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-10290 | |||||||||
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タイトル | Structure of Fanconi anaemia core complex (consensus map) | |||||||||
![]() | This is the post processed consensus map. To see the fit of model into map, please use the focussed maps for top, middle, bottom and superimposed consensus maps with and without T=5 on middle map. | |||||||||
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![]() | Fanconi Anaemia core complex / E3 ligase / DNA repair / LIGASE | |||||||||
機能・相同性 | ![]() PKR-mediated signaling / Fanconi Anemia Pathway in DNA repair / Fanconi Anemia Pathway / Fanconi anaemia nuclear complex / protein monoubiquitination / interstrand cross-link repair / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / DNA repair / DNA damage response ...PKR-mediated signaling / Fanconi Anemia Pathway in DNA repair / Fanconi Anemia Pathway / Fanconi anaemia nuclear complex / protein monoubiquitination / interstrand cross-link repair / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / DNA repair / DNA damage response / nucleoplasm / nucleus 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: 4.2 Å | |||||||||
![]() | Shakeel S / Rajendra E | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of the Fanconi anaemia monoubiquitin ligase complex. 著者: Shabih Shakeel / Eeson Rajendra / Pablo Alcón / Francis O'Reilly / Dror S Chorev / Sarah Maslen / Gianluca Degliesposti / Christopher J Russo / Shaoda He / Chris H Hill / J Mark Skehel / ...著者: Shabih Shakeel / Eeson Rajendra / Pablo Alcón / Francis O'Reilly / Dror S Chorev / Sarah Maslen / Gianluca Degliesposti / Christopher J Russo / Shaoda He / Chris H Hill / J Mark Skehel / Sjors H W Scheres / Ketan J Patel / Juri Rappsilber / Carol V Robinson / Lori A Passmore / ![]() ![]() 要旨: The Fanconi anaemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks, and responds to replication stress. Genetic inactivation of this pathway by mutation ...The Fanconi anaemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks, and responds to replication stress. Genetic inactivation of this pathway by mutation of genes encoding FA complementation group (FANC) proteins impairs development, prevents blood production and promotes cancer. The key molecular step in the FA pathway is the monoubiquitination of a pseudosymmetric heterodimer of FANCD2-FANCI by the FA core complex-a megadalton multiprotein E3 ubiquitin ligase. Monoubiquitinated FANCD2 then recruits additional protein factors to remove the DNA crosslink or to stabilize the stalled replication fork. A molecular structure of the FA core complex would explain how it acts to maintain genome stability. Here we reconstituted an active, recombinant FA core complex, and used cryo-electron microscopy and mass spectrometry to determine its structure. The FA core complex comprises two central dimers of the FANCB and FA-associated protein of 100 kDa (FAAP100) subunits, flanked by two copies of the RING finger subunit, FANCL. These two heterotrimers act as a scaffold to assemble the remaining five subunits, resulting in an extended asymmetric structure. Destabilization of the scaffold would disrupt the entire complex, resulting in a non-functional FA pathway. Thus, the structure provides a mechanistic basis for the low numbers of patients with mutations in FANCB, FANCL and FAAP100. Despite a lack of sequence homology, FANCB and FAAP100 adopt similar structures. The two FANCL subunits are in different conformations at opposite ends of the complex, suggesting that each FANCL has a distinct role. This structural and functional asymmetry of dimeric RING finger domains may be a general feature of E3 ligases. The cryo-electron microscopy structure of the FA core complex provides a foundation for a detailed understanding of its E3 ubiquitin ligase activity and DNA interstrand crosslink repair. | |||||||||
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 | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 38.1 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 60.8 KB 60.8 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 20.8 KB | 表示 | ![]() |
画像 | ![]() | 66.8 KB | ||
マスクデータ | ![]() | 767.6 MB | ![]() | |
Filedesc metadata | ![]() | 7.2 KB | ||
その他 | ![]() ![]() ![]() ![]() ![]() | 620.3 MB 620.3 MB 620.3 MB 622.1 MB 621.7 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 635.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 634.7 KB | 表示 | |
XML形式データ | ![]() | 30 KB | 表示 | |
CIF形式データ | ![]() | 38.7 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 | ![]() 6sriMC ![]() 6srsC 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 | |
電子顕微鏡画像生データ | ![]() Data size: 13.2 TB Data #1: Unaligned movies for FA core complex and symmetric complex [micrographs - multiframe] Data #2: Unaligned movies for FA core complex and symmetric complex [micrographs - multiframe]) |
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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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注釈 | This is the post processed consensus map. To see the fit of model into map, please use the focussed maps for top, middle, bottom and superimposed consensus maps with and without T=5 on middle map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-マスク #1
ファイル | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: This is the map from auto refinement in Relion
ファイル | emd_10290_additional_1.map | ||||||||||||
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注釈 | This is the map from auto refinement in Relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Consensus map refined with T=5 value in Relion,...
ファイル | emd_10290_additional_2.map | ||||||||||||
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注釈 | Consensus map refined with T=5 value in Relion, post processed and superimposed on middle map using Proshade from ccpem. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: This is the map from auto refinement in Relion.
ファイル | emd_10290_additional_3.map | ||||||||||||
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注釈 | This is the map from auto refinement in Relion. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: This is half1 map from auto refinement in Relion.
ファイル | emd_10290_half_map_1.map | ||||||||||||
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注釈 | This is half1 map from auto refinement in Relion. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: This is half2 map from auto refinement in Relion.
ファイル | emd_10290_half_map_2.map | ||||||||||||
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注釈 | This is half2 map from auto refinement in Relion. | ||||||||||||
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 : Fanconi anaemia core complex
+超分子 #1: Fanconi anaemia core complex
+分子 #1: Unassigned secondary structure elements (central region, proposed...
+分子 #2: Unassigned secondary structure elements (central region, proposed...
+分子 #3: Unassigned secondary structure elements (central region, proposed...
+分子 #4: Unassigned secondary structure elements (central region, proposed...
+分子 #5: Unassigned secondary structure elements (central region, proposed...
+分子 #6: Unassigned secondary structure elements (central region, proposed...
+分子 #7: Unassigned secondary structure elements (central region, proposed...
+分子 #8: Unassigned secondary structure elements (central region, proposed...
+分子 #9: Unassigned secondary structure elements (central region, proposed...
+分子 #10: Unassigned secondary structure elements (central region, proposed...
+分子 #11: Unassigned secondary structure elements (central region, proposed...
+分子 #12: Unassigned secondary structure elements (proposed FANCB)
+分子 #13: Unassigned secondary structure elements (proposed FAAP100)
+分子 #14: Unassigned secondary structure elements (proposed FANCB)
+分子 #15: Unassigned secondary structure elements (proposed FAAP100)
+分子 #16: Unassigned secondary structure elements (base region, proposed FA...
+分子 #17: Unassigned secondary structure elements (base region, proposed FA...
+分子 #18: Unassigned secondary structure elements (base region, proposed FA...
+分子 #19: Unassigned secondary structure elements (base region, proposed FA...
+分子 #20: Unassigned secondary structure elements (base region, proposed FA...
+分子 #21: Unassigned secondary structure elements (base region, proposed FA...
+分子 #22: Unassigned secondary structure elements (base region, proposed FA...
+分子 #23: Unassigned secondary structure elements (base region, proposed FA...
+分子 #24: Fanconi anaemia protein FANCL
+分子 #25: base region, proposed FANCF
+分子 #26: Unassigned secondary structure elements (top region, proposed FANCG)
+分子 #27: Unassigned secondary structure elements (top region, proposed FANCG)
-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 | 0.7 mg/mL |
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緩衝液 | pH: 8 / 詳細: 50 mM HEPES pH 8.0, ~500 mM NaCl, 1 mM TCEP |
グリッド | モデル: Quantifoil, UltrAuFoil, R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: PLASMA CLEANING / 前処理 - 時間: 30 sec. / 詳細: Argon: 9 parts Oxygen: 1 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV 詳細: Blot time: 3 to 4.5 s Wait time: 0 s Drain time: 0 s Force: -10 N. |
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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: FEI FALCON III (4k x 4k) 検出モード: COUNTING / 実像数: 4145 / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 50.0 µm / 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): -4.0 µm / 最小 デフォーカス(公称値): -1.8 µm / 倍率(公称値): 75000 |
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
精密化 | プロトコル: OTHER |
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得られたモデル | ![]() PDB-6sri: |