+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6fdk | |||||||||
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タイトル | Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin | |||||||||
要素 |
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キーワード | HYDROLASE (加水分解酵素) / ChlaDUB1 / CE protease / DUB / Ubiquitin. (ユビキチン) | |||||||||
機能・相同性 | 機能・相同性情報 deNEDDylase activity / deSUMOylase activity / protein desumoylation / protein deneddylation / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development ...deNEDDylase activity / deSUMOylase activity / protein desumoylation / protein deneddylation / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / protein deubiquitination / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / グリコーゲン合成 / 宿主 / 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) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / neuron projection morphogenesis / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / Evasion by RSV of host interferon responses / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD 類似検索 - 分子機能 | |||||||||
生物種 | Chlamydia trachomatis 434/Bu (トラコーマクラミジア) Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.6 Å | |||||||||
データ登録者 | Ramirez, Y. / Kisker, C. | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: ChemMedChem / 年: 2018 タイトル: Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis. 著者: Ramirez, Y.A. / Adler, T.B. / Altmann, E. / Klemm, T. / Tiesmeyer, C. / Sauer, F. / Kathman, S.G. / Statsyuk, A.V. / Sotriffer, C. / Kisker, C. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6fdk.cif.gz | 136.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6fdk.ent.gz | 104.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6fdk.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fd/6fdk ftp://data.pdbj.org/pub/pdb/validation_reports/fd/6fdk | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 30454.164 Da / 分子数: 1 / 変異: C174A, C226S, C386A / 由来タイプ: 組換発現 由来: (組換発現) Chlamydia trachomatis 434/Bu (トラコーマクラミジア) 遺伝子: cdu1, CTL0247 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: B0B9A0, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ |
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#2: タンパク質 | 分子量: 8519.778 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: UBB 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P0CG47 |
#3: 化合物 | ChemComp-CL / |
#4: 化合物 | ChemComp-AYE / |
#5: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.05 Å3/Da / 溶媒含有率: 39.91 % / 解説: Blade like |
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結晶化 | 温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M MES pH 6.5, 12% PEG 20000 |
-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: シンクロトロン / サイト: ESRF / ビームライン: ID23-1 / 波長: 0.98 Å |
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2017年11月20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: 0.98 Å / 相対比: 1 |
反射 | 解像度: 1.6→46.22 Å / Num. obs: 41326 / % possible obs: 98.86 % / 冗長度: 6.7 % / Biso Wilson estimate: 23.74 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02739 / Rrim(I) all: 0.07178 / Net I/σ(I): 17.06 |
反射 シェル | 解像度: 1.6→1.657 Å / 冗長度: 7 % / Mean I/σ(I) obs: 1.32 / Num. unique obs: 4140 / CC1/2: 0.561 / Rpim(I) all: 0.6474 / % possible all: 99.9 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5B5Q 解像度: 1.6→46.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.352 / SU ML: 0.07 / 交差検証法: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.092 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 23.148 Å2
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精密化ステップ | サイクル: 1 / 解像度: 1.6→46.22 Å
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拘束条件 |
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