+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2y5b | ||||||
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タイトル | Structure of USP21 in complex with linear diubiquitin-aldehyde | ||||||
要素 |
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キーワード | PROTEIN BINDING/HYDROLASE / PROTEIN BINDING-HYDROLASE COMPLEX / UBIQUITIN / UBIQUITIN SPECIFIC PROTEASE / USP / NEDD8 / ISG15 / CELL SIGNALING | ||||||
機能・相同性 | 機能・相同性情報 deNEDDylase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / TNFR1-induced proapoptotic signaling / fat pad development / female gonad development / seminiferous tubule development / male meiosis I ...deNEDDylase activity / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / TNFR1-induced proapoptotic signaling / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process / energy homeostasis / regulation of proteasomal protein catabolic process / cysteine-type peptidase activity / 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 / transcription initiation-coupled chromatin remodeling / 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 / 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 / neuron projection morphogenesis / 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) / 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 / positive regulation of protein ubiquitination / 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 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å | ||||||
データ登録者 | Ye, Y. / Akutsu, M. / Reyes-Turcu, F. / Enchev, R.I. / Wilkinson, K.D. / Komander, D. | ||||||
引用 | ジャーナル: Embo Rep. / 年: 2011 タイトル: Polyubiquitin Binding and Cross-Reactivity in the Usp Domain Deubiquitinase Usp21. 著者: Ye, Y. / Akutsu, M. / Reyes-Turcu, F. / Enchev, R.I. / Wilkinson, K.D. / Komander, D. | ||||||
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 | 2y5b.cif.gz | 191.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2y5b.ent.gz | 148 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2y5b.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 | 2y5b_validation.pdf.gz | 472.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2y5b_full_validation.pdf.gz | 488.5 KB | 表示 | |
XML形式データ | 2y5b_validation.xml.gz | 33.4 KB | 表示 | |
CIF形式データ | 2y5b_validation.cif.gz | 45.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y5b ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y5b | HTTPS FTP |
-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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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 41744.570 Da / 分子数: 2 / 断片: CATALYTIC DOMAIN, RESIDUES 196-565 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): ROSETTA2 PLYSS 参照: UniProt: Q9UK80, EC: 3.1.2.15, ubiquitinyl hydrolase 1 #2: タンパク質 | 分子量: 17200.750 Da / 分子数: 2 / 断片: LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152 / Mutation: YES / 由来タイプ: 組換発現 詳細: NON-CLEAVABLE LINEAR DIUBIQUITIN ALDEHYDE WITH G76H MUTATION 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PTYB2 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): ROSETTA2 PLYSS / 参照: UniProt: P0CG47 #3: 化合物 | #4: 化合物 | ChemComp-SO4 / #5: 水 | ChemComp-HOH / | 構成要素の詳細 | ENGINEERED | 非ポリマーの詳細 | AMINO-ACETALDEHY | |
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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: 2.36 Å3/Da / 溶媒含有率: 48 % / 解説: NONE |
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結晶化 | pH: 7.4 / 詳細: 15% PEG8000, 0.2 M NH4SO4, pH 7.4 |
-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: ID23-2 / 波長: 1 |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2009年5月9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: 1 Å / 相対比: 1 |
反射 | 解像度: 2.7→49.8 Å / Num. obs: 24840 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / 冗長度: 2.9 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8 |
反射 シェル | 解像度: 2.7→2.85 Å / 冗長度: 3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / % possible all: 86.2 |
-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 ENTRIES 2HD5 AND 1UBQ 解像度: 2.7→45 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.829 / SU B: 14.82 / SU ML: 0.306 / 交差検証法: THROUGHOUT / ESU R Free: 0.438 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. COVALENT LINK BETWEEN C221 IN CHAIN A,E AND GLZ152 IN CHAIN B,F.
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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: 20.315 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.7→45 Å
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拘束条件 |
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