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基本情報
登録情報 | ![]() | |||||||||
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タイトル | Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD) | |||||||||
![]() | composite map of the ubiquitin unfolded state 'uD' | |||||||||
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機能・相同性 | ![]() SCF complex disassembly in response to cadmium stress / Josephin domain DUBs / RAS processing / Ovarian tumor domain proteases / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / endoplasmic reticulum membrane fusion / UCH proteinases / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Pexophagy ...SCF complex disassembly in response to cadmium stress / Josephin domain DUBs / RAS processing / Ovarian tumor domain proteases / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / endoplasmic reticulum membrane fusion / UCH proteinases / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Pexophagy / Interleukin-1 signaling / Aggrephagy / Doa10p ubiquitin ligase complex / DNA replication termination / stress-induced homeostatically regulated protein degradation pathway / sister chromatid biorientation / positive regulation of mitochondrial fusion / ribophagy / Peroxisomal protein import / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / RQC complex / protein localization to vacuole / protein-containing complex disassembly / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / HSF1 activation / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / E3 ubiquitin ligases ubiquitinate target proteins / nonfunctional rRNA decay / protein phosphatase regulator activity / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / piecemeal microautophagy of the nucleus / mating projection tip / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / replisome / ribosome-associated ubiquitin-dependent protein catabolic process / nuclear outer membrane-endoplasmic reticulum membrane network / retrograde protein transport, ER to cytosol / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / protein quality control for misfolded or incompletely synthesized proteins / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / autophagosome maturation / Dual incision in TC-NER / polyubiquitin modification-dependent protein binding / mRNA transport / Ub-specific processing proteases / ERAD pathway / ATP metabolic process / Neutrophil degranulation / rescue of stalled ribosome / ubiquitin binding / macroautophagy / modification-dependent protein catabolic process / positive regulation of protein localization to nucleus / protein tag activity / ubiquitin-dependent protein catabolic process / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol 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: 3.6 Å | |||||||||
![]() | Lee HG / Lima CD | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. 著者: Hyein G Lee / Abigail A Lemmon / Christopher D Lima / ![]() 要旨: The Ufd1/Npl4/Cdc48 complex is a universal protein segregase that plays key roles in eukaryotic cellular processes. Its functions orchestrating the clearance or removal of polyubiquitylated targets ...The Ufd1/Npl4/Cdc48 complex is a universal protein segregase that plays key roles in eukaryotic cellular processes. Its functions orchestrating the clearance or removal of polyubiquitylated targets are established; however, prior studies suggest that the complex also targets substrates modified by the ubiquitin-like protein SUMO. Here, we show that interactions between Ufd1 and SUMO enhance unfolding of substrates modified by SUMO-polyubiquitin hybrid chains by the budding yeast Ufd1/Npl4/Cdc48 complex compared to substrates modified by polyubiquitin chains, a difference that is accentuated when the complex has a choice between these substrates. Incubating Ufd1/Npl4/Cdc48 with a substrate modified by a SUMO-polyubiquitin hybrid chain produced a series of single-particle cryo-EM structures that reveal features of interactions between Ufd1/Npl4/Cdc48 and ubiquitin prior to and during unfolding of ubiquitin. These results are consistent with cellular functions for SUMO and ubiquitin modifications and support a physical model wherein Ufd1/Npl4/Cdc48, SUMO, and ubiquitin conjugation pathways converge to promote clearance of proteins modified with SUMO and polyubiquitin. | |||||||||
履歴 |
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構造の表示
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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 | ![]() | 25.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 53.9 KB 53.9 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 13.6 KB | 表示 | ![]() |
画像 | ![]() | 96 KB | ||
その他 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 17.5 MB 9.9 MB 171.2 MB 171.2 MB 8 MB 13.5 MB 170.7 MB 170.7 MB 171.4 MB 171.2 MB 12.2 MB 171.2 MB 171.4 MB 171.5 MB 171.4 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 728.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 727.9 KB | 表示 | |
XML形式データ | ![]() | 21.6 KB | 表示 | |
CIF形式データ | ![]() | 28.4 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
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 | composite map of the ubiquitin unfolded state 'uD' | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.064 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
+追加マップ: post-processed overall refinement map of the ubiquitin unfolded...
+追加マップ: post-processed focused refinement map of the Ufd1/Npl4 tower...
+追加マップ: focused refinement half map 1 of Cdc48 of...
+追加マップ: focused refinement half map 1 of the Ufd1/Npl4...
+追加マップ: post-processed focused refinement map of upper Ufd1/Npl4 tower...
+追加マップ: post-processed focused refinement map of Cdc48 of the...
+追加マップ: focused refinement half map 1 of upper Ufd1/Npl4...
+追加マップ: focused refinement half map 2 of upper Ufd1/Npl4...
+追加マップ: focused refinement half map 2 of the D1/D2...
+追加マップ: focused refinement half map 2 of the Ufd1/Npl4...
+追加マップ: post-processed focused refinement map of the D1/D2 ATPase...
+追加マップ: focused refinement half map 2 of Cdc48 of...
+追加マップ: focused refinement half map 1 of the D1/D2...
+ハーフマップ: overall refinement half map 2 of the ubiquitin unfolded state 'uD'
+ハーフマップ: overall refinement half map 1 of the ubiquitin unfolded state 'uD'
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試料の構成要素
+全体 : Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three u...
+超分子 #1: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three u...
+超分子 #2: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three u...
+超分子 #3: Cdc48 hexamer
+超分子 #4: Three folded ubiqutin moieties and one unfolded ubiquitin bound t...
+超分子 #5: D1/D2 ATPase domains of the Cdc48 hexamer
+超分子 #6: Three folded Ubiqutin moieties bound to Npl4
+分子 #1: Cell division control protein 48
+分子 #2: Nuclear protein localization protein 4
+分子 #3: Ubiquitin fusion degradation protein 1
+分子 #4: Ubiquitin
+分子 #5: ADENOSINE-5'-TRIPHOSPHATE
+分子 #6: ADENOSINE-5'-DIPHOSPHATE
+分子 #7: 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 | 2 mg/mL |
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緩衝液 | pH: 8 詳細: 20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 295 K / 装置: FEI VITROBOT MARK IV / 詳細: 8 s wait, 4 s blot before plunging. |
詳細 | Ufd1/Npl4/Cdc48 was pre-incubated with SUMO-ubiquitin(K48polyUb)-mEOS and ATP |
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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 (6k x 4k) / 平均電子線量: 70.577 e/Å2 |
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 最大 デフォーカス(公称値): 2.8000000000000003 µm 最小 デフォーカス(公称値): 1.2 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |