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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: 6aqr | ||||||
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タイトル | SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin | ||||||
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![]() | HYDROLASE / histone deubiquitination / ubiquitin / transcription | ||||||
機能・相同性 | ![]() RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus ...RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / Ub-specific processing proteases / nuclear pore / mRNA export from nucleus / 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 / RNA splicing / 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 / 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 / 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 / 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 / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / transcription elongation by RNA polymerase II / Negative regulation of FGFR2 signaling 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Morrow, M.E. / Morgan, M.T. / Wolberger, C. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins. 著者: Morrow, M.E. / Morgan, M.T. / Clerici, M. / Growkova, K. / Yan, M. / Komander, D. / Sixma, T.K. / Simicek, M. / Wolberger, C. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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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 | ![]() | 179.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 138.4 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 | ![]() | 459.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 466.2 KB | 表示 | |
XML形式データ | ![]() | 31.8 KB | 表示 | |
CIF形式データ | ![]() | 44.9 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 | ![]() 3mhsS S: 精密化の開始モデル |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
-タンパク質 , 3種, 3分子 ABD
#1: タンパク質 | 分子量: 54001.566 Da / 分子数: 1 / 変異: C146A / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 株: ATCC 204508 / S288c / 遺伝子: UBP8, YMR223W, YM9959.05 / 発現宿主: ![]() ![]() |
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#2: タンパク質 | 分子量: 11094.497 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 株: ATCC 204508 / S288c / 遺伝子: SUS1, YBR111W-A / 発現宿主: ![]() ![]() |
#4: タンパク質 | 分子量: 8576.831 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
-SAGA-associated factor ... , 2種, 2分子 CE
#3: タンパク質 | 分子量: 11297.625 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 株: ATCC 204508 / S288c / 遺伝子: SGF11, YPL047W / 発現宿主: ![]() ![]() |
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#5: タンパク質 | 分子量: 10824.273 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 株: ATCC 204508 / S288c / 遺伝子: SGF73, YGL066W / 発現宿主: ![]() ![]() |
-非ポリマー , 2種, 272分子 


#6: 化合物 | ChemComp-ZN / #7: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.39 Å3/Da / 溶媒含有率: 48.58 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 詳細: 0.1 M HEPES pH 7.0 17% PEG3350 0.1 M ammonium sulfate |
-データ収集
回折 | 平均測定温度: 100 K | ||||||||||||||||||||||||||||||
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放射光源 | 由来: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年5月7日 | ||||||||||||||||||||||||||||||
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray | ||||||||||||||||||||||||||||||
放射波長 | 波長: 0.9794 Å / 相対比: 1 | ||||||||||||||||||||||||||||||
反射 | 解像度: 2.1→46.92 Å / Num. obs: 53790 / % possible obs: 99.2 % / 冗長度: 5.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.043 / Rrim(I) all: 0.103 / Net I/σ(I): 13.3 / Num. measured all: 304961 / Scaling rejects: 66 | ||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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-位相決定
位相決定 | 手法: ![]() | |||||||||
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Phasing MR |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 3MHS 解像度: 2.1→76.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2369 / WRfactor Rwork: 0.1882 / FOM work R set: 0.8044 / SU B: 5.604 / SU ML: 0.144 / SU R Cruickshank DPI: 0.2222 / SU Rfree: 0.1913 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.191 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: U VALUES : REFINED INDIVIDUALLY
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 123.66 Å2 / Biso mean: 34.399 Å2 / Biso min: 2.52 Å2
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精密化ステップ | サイクル: final / 解像度: 2.1→76.15 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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