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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: PDB / ID: 9hnw | |||||||||
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| タイトル | USP1-UAF1 bound to Lys63-linked diubiquitin | |||||||||
要素 |
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キーワード | HYDROLASE / USP1 / deubiquitinating enzyme / cysteine protease / complex | |||||||||
| 機能・相同性 | 機能・相同性情報regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / monoubiquitinated protein deubiquitination / deubiquitinase activator activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / skeletal system morphogenesis ...regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / monoubiquitinated protein deubiquitination / deubiquitinase activator activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / skeletal system morphogenesis / mitochondrion transport along microtubule / skin development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / homeostasis of number of cells / protein deubiquitination / embryonic organ development / single fertilization / regulation of DNA repair / response to UV / positive regulation of double-strand break repair via homologous recombination / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / 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 / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / 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 / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / positive regulation of epithelial cell proliferation / 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 / skeletal system development / regulation of mitochondrial membrane potential / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / positive regulation of receptor signaling pathway via JAK-STAT 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: 3.04 Å | |||||||||
データ登録者 | Keijzer, N. / Sakoltchik, J. / Sixma, T.K. | |||||||||
| 資金援助 | オランダ, 2件
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引用 | ジャーナル: Nat Commun / 年: 2025タイトル: USP1/UAF1 targets polyubiquitinated PCNA with an exo-cleavage mechanism that can temporarily enrich for monoubiquitinated PCNA. 著者: Niels Keijzer / Jan Sakoltchik / Kaustav Majumder / Nina van Lil / Farid El Oualid / Alexander Fish / Titia K Sixma / ![]() 要旨: DNA damage tolerance (DDT) is an important pathway that allows cells to bypass DNA lesions during replication. DDT is orchestrated by ubiquitination of PCNA, where monoubiquitinated PCNA (PCNA-Ub) ...DNA damage tolerance (DDT) is an important pathway that allows cells to bypass DNA lesions during replication. DDT is orchestrated by ubiquitination of PCNA, where monoubiquitinated PCNA (PCNA-Ub) initiates recruitment of TLS polymerases but also serves as a substrate for further ubiquitination, forming K63-polyubiquitinated PCNA that leads to HR-mediated bypass mechanisms. Recent work on USP1/UAF1 inhibition revealed that formation of K48-linked chains also occurs on PCNA, resulting in its proteasomal degradation. USP1/UAF1 is established as deubiquitinating enzyme (DUB) for PCNA-Ub, but little is known about removal of ubiquitin chains on PCNA. Here we show that USP1/UAF1 cleaves both K48 and K63-linked ubiquitin chains on PCNA efficiently, using an exo-cleavage mechanism. Kinetic analysis reveals that USP1/UAF1 prefers cleaving the ubiquitin-ubiquitin bond over cleavage of the ubiquitin-PCNA bond and therefore treats poly- and monoubiquitinated PCNA as different substrates. A cryo-EM structure of USP1/UAF1 with a K63-diubiquitin and structure-based mutagenesis suggests that this mechanistic preference is maintained in evolution. This unusual mechanism can cause temporal enrichment of monoubiquitinated PCNA during polyubiquitination. It will be interesting to see how this affects DDT pathway balance. | |||||||||
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構造の表示
| 構造ビューア | 分子: Molmil Jmol/JSmol |
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ダウンロードとリンク
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ダウンロード
| PDBx/mmCIF形式 | 9hnw.cif.gz | 231.8 KB | 表示 | PDBx/mmCIF形式 |
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| PDB形式 | pdb9hnw.ent.gz | 175.5 KB | 表示 | PDB形式 |
| PDBx/mmJSON形式 | 9hnw.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 | 9hnw_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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| 文書・詳細版 | 9hnw_full_validation.pdf.gz | 1.2 MB | 表示 | |
| XML形式データ | 9hnw_validation.xml.gz | 49.3 KB | 表示 | |
| CIF形式データ | 9hnw_validation.cif.gz | 75.2 KB | 表示 | |
| アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/hn/9hnw ftp://data.pdbj.org/pub/pdb/validation_reports/hn/9hnw | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 52316MC 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 ( |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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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
| #1: タンパク質 | 分子量: 91785.992 Da / 分子数: 1 / 変異: G670A, G671A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: USP1発現宿主: ![]() 参照: UniProt: O94782, ubiquitinyl hydrolase 1 |
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| #2: タンパク質 | 分子量: 80130.719 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: WDR48, KIAA1449, UAF1発現宿主: ![]() 参照: UniProt: Q8TAF3 |
| #3: タンパク質 | 分子量: 8604.884 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P0CG47 |
| #4: タンパク質 | 分子量: 8547.770 Da / 分子数: 1 / 変異: K63(DAB) / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P0CG47 |
| #5: 化合物 | ChemComp-ZN / |
| 研究の焦点であるリガンドがあるか | N |
| 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 |
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試料調製
| 構成要素 | 名称: USP1-UAF1 bound to Lys63-linked diubiquitin / タイプ: COMPLEX / Entity ID: #1-#2, #4 / 由来: RECOMBINANT | ||||||||||||||||||||
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| 分子量 | 実験値: NO | ||||||||||||||||||||
| 由来(天然) | 生物種: Homo sapiens (ヒト) | ||||||||||||||||||||
| 由来(組換発現) | 生物種: ![]() | ||||||||||||||||||||
| 緩衝液 | pH: 7.5 | ||||||||||||||||||||
| 緩衝液成分 |
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| 試料 | 濃度: 0.75 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||
| 試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / 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: 277.15 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: TFS KRIOS 詳細: Collected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN) |
| 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): 10500 X / 最大 デフォーカス(公称値): 2400 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE |
| 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 | 平均露光時間: 2.71 sec. / 電子線照射量: 50 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: 5833 |
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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: 3110350 | ||||||
| 3次元再構成 | 解像度: 3.04 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 299304 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT | ||||||
| 精密化 | 最高解像度: 3.04 Å |
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万見について




Homo sapiens (ヒト)
オランダ, 2件
引用
PDBj




















FIELD EMISSION GUN