+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3ns8 | ||||||
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タイトル | Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5 | ||||||
要素 | Ubiquitinユビキチン | ||||||
キーワード | SIGNALING PROTEIN / Diubiquitin / isopeptide bond | ||||||
機能・相同性 | 機能・相同性情報 : / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation ...: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / cytosolic ribosome / グリコーゲン合成 / 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 / 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 / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / 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 / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome 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: 1.707 Å | ||||||
データ登録者 | Zhang, D. / LaRonde-LeBlanc, N. / Fushman, D. | ||||||
引用 | ジャーナル: Biochim.Biophys.Acta / 年: 2012 タイトル: Structural and biochemical studies of the open state of Lys48-linked diubiquitin. 著者: Lai, M.Y. / Zhang, D. / Laronde-Leblanc, N. / Fushman, 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 | 3ns8.cif.gz | 47.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3ns8.ent.gz | 32.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3ns8.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/ns/3ns8 ftp://data.pdbj.org/pub/pdb/validation_reports/ns/3ns8 | HTTPS FTP |
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-関連構造データ
関連構造データ | 1ubqS 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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詳細 | The biological unit is two monomers linked by an isopeptide bond between the carboxy-terminal glycine 76 of one monomer, and the lysine 48 side chain of the second monomer. |
-要素
#1: タンパク質 | 分子量: 8576.831 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RPS27A / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P62988, UniProt: P0CG48*PLUS #2: 化合物 | #3: 化合物 | ChemComp-EPE / | #4: 水 | ChemComp-HOH / | |
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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: 1.85 Å3/Da / 溶媒含有率: 33.58 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 詳細: HEPES, PEG 8000, Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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: APS / ビームライン: 24-ID-E / 波長: 0.97927 Å |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2007年6月14日 |
放射 | モノクロメーター: single crystal Si(111) side bounce monochromator 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: 0.97927 Å / 相対比: 1 |
反射 | 解像度: 1.707→18.3 Å / Num. all: 13670 / Num. obs: 12906 / % possible obs: 94.41 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / 冗長度: 4.5 % / Biso Wilson estimate: 17.44 Å2 / Rsym value: 0.073 / Net I/σ(I): 17.3 |
反射 シェル | 解像度: 1.71→1.76 Å / 冗長度: 3.7 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 968 / Rsym value: 0.18 / % possible all: 72.7 |
-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: 1UBQ 解像度: 1.707→18.293 Å / SU ML: 0.22 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 1.36 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 65.935 Å2 / ksol: 0.406 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 21.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.707→18.293 Å
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拘束条件 |
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LS精密化 シェル |
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