+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4ldt | ||||||
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タイトル | The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub | ||||||
要素 |
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キーワード | HYDROLASE REGULATOR / isopeptidase / ubiquitin-conjugating / post-translational modification / ubiquitin / ubiquitin-aldehyde | ||||||
機能・相同性 | 機能・相同性情報 Ovarian tumor domain proteases / ubiquitin-protein transferase inhibitor activity / negative regulation of double-strand break repair / deNEDDylase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K48-linked deubiquitination / E2 ubiquitin-conjugating enzyme / protein deubiquitination / ubiquitin conjugating enzyme activity / protein autoubiquitination ...Ovarian tumor domain proteases / ubiquitin-protein transferase inhibitor activity / negative regulation of double-strand break repair / deNEDDylase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K48-linked deubiquitination / E2 ubiquitin-conjugating enzyme / protein deubiquitination / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / 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 / Membrane binding and targetting of GAG proteins / positive regulation of TORC1 signaling / 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 / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / 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 / 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) / 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 / ubiquitin binding / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / 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 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Caenorhabditis elegans (センチュウ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.901 Å | ||||||
データ登録者 | Wiener, R. / DiBello, A.T. / Lombardi, P.M. / Guzzo, C.M. / Zhang, X. / Matunis, M.J. / Wolberger, C. | ||||||
引用 | ジャーナル: Nat.Struct.Mol.Biol. / 年: 2013 タイトル: E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1. 著者: Wiener, R. / Dibello, A.T. / Lombardi, P.M. / Guzzo, C.M. / Zhang, X. / Matunis, M.J. / Wolberger, 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 | 4ldt.cif.gz | 242.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4ldt.ent.gz | 193.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4ldt.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 | 4ldt_validation.pdf.gz | 463 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4ldt_full_validation.pdf.gz | 466.3 KB | 表示 | |
XML形式データ | 4ldt_validation.xml.gz | 25 KB | 表示 | |
CIF形式データ | 4ldt_validation.cif.gz | 36 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ld/4ldt ftp://data.pdbj.org/pub/pdb/validation_reports/ld/4ldt | HTTPS FTP |
-関連構造データ
関連構造データ | 4dhzS S: 精密化の開始モデル |
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類似構造データ |
-リンク
-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 , 4種, 4分子 ABCD
#1: タンパク質 | 分子量: 32795.637 Da / 分子数: 1 / 断片: SEE REMARK 999 / 由来タイプ: 組換発現 由来: (組換発現) Homo sapiens (ヒト), (組換発現) Caenorhabditis elegans (センチュウ) 遺伝子: OTUB1, OTB1, OTU1, HSPC263, C25D7.8, otub-1 / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: Q96FW1, UniProt: Q9XVR6, ubiquitinyl hydrolase 1 |
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#2: タンパク質 | 分子量: 8560.831 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: UBC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG48 |
#3: タンパク質 | 分子量: 16796.213 Da / 分子数: 1 / Mutation: C85S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62837, ubiquitin-protein ligase |
#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) Homo sapiens (ヒト) / 遺伝子: UBC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG48 |
-非ポリマー , 3種, 321分子
#5: 化合物 | ChemComp-EDO / #6: 化合物 | ChemComp-MG / | #7: 水 | ChemComp-HOH / | |
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-詳細
配列の詳細 | THE UBIQUITIN THIOESTERASE CONSTRUCT IS A CHIMERA COMPRISING RESIDUES 1-45 OF UNP Q96FW1 AND ...THE UBIQUITIN THIOESTERA |
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-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: 2.41 Å3/Da / 溶媒含有率: 48.86 % |
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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 / pH: 6 詳細: 1:1 mix of 12 mg/mL purified complex and well solution (100 mM Bis-Tris, pH 6.0, 200 mM magnesium chloride, 22% PEG3350), crystals appeared in about 2 to 3 days, cryoprotection with well ...詳細: 1:1 mix of 12 mg/mL purified complex and well solution (100 mM Bis-Tris, pH 6.0, 200 mM magnesium chloride, 22% PEG3350), crystals appeared in about 2 to 3 days, cryoprotection with well solution + 10% ethylene glycol, flash frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-データ収集
回折 | 平均測定温度: 77 K |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-D / 波長: 1 Å |
検出器 | タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2012年3月11日 |
放射 | モノクロメーター: Double crystal cryo-cooled Si(111) 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: 1 Å / 相対比: 1 |
反射 | 解像度: 1.901→33.65 Å / Num. all: 51642 / Num. obs: 51582 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 8 % / Rsym value: 0.13 / Net I/σ(I): 8.5 |
反射 シェル | 解像度: 1.901→1.93 Å / 冗長度: 3.1 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.57 / % possible all: 95.4 |
-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: PDB ENTRY 4DHZ 解像度: 1.901→33.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.665 / SU ML: 0.099 / 交差検証法: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.137 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 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 / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 30.507 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.901→33.65 Å
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拘束条件 |
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