+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4s1z | ||||||
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タイトル | Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin | ||||||
要素 |
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キーワード | HYDROLASE / zinc finger / Protease / Ubiquitin binding | ||||||
機能・相同性 | 機能・相同性情報 protein K33-linked deubiquitination / protein K29-linked deubiquitination / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / Ovarian tumor domain proteases / Degradation of beta-catenin by the destruction complex / regulation of cell morphogenesis / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / Peptide chain elongation / Selenocysteine synthesis ...protein K33-linked deubiquitination / protein K29-linked deubiquitination / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / Ovarian tumor domain proteases / Degradation of beta-catenin by the destruction complex / regulation of cell morphogenesis / protein K63-linked deubiquitination / K63-linked polyubiquitin modification-dependent protein binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / positive regulation of Wnt signaling pathway / 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 / cytoskeleton organization / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / cytosolic ribosome / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / InlB-mediated entry of Listeria monocytogenes into host cell / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Bos taurus (ウシ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.03 Å | ||||||
データ登録者 | Kristariyanto, Y.A. / Abdul Rehman, S.A. / Campbell, D.G. / Morrice, N.A. / Johnson, C. / Toth, R. / Kulathu, Y. | ||||||
引用 | ジャーナル: Mol.Cell / 年: 2015 タイトル: K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin. 著者: Kristariyanto, Y.A. / Abdul Rehman, S.A. / Campbell, D.G. / Morrice, N.A. / Johnson, C. / Toth, R. / Kulathu, Y. | ||||||
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 | 4s1z.cif.gz | 105.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4s1z.ent.gz | 79.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4s1z.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 | 4s1z_validation.pdf.gz | 477 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4s1z_full_validation.pdf.gz | 478.1 KB | 表示 | |
XML形式データ | 4s1z_validation.xml.gz | 17.4 KB | 表示 | |
CIF形式データ | 4s1z_validation.cif.gz | 24.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/s1/4s1z ftp://data.pdbj.org/pub/pdb/validation_reports/s1/4s1z | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 8576.831 Da / 分子数: 5 / 断片: residues 1-76 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBA52, UBCEP2, ZRANB1 / プラスミド: pGEX6P1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P62987 #2: タンパク質・ペプチド | 分子量: 4098.710 Da / 分子数: 5 / 断片: RanBP2-type 1 zinc finger domain residues 2-33 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 組織: blood / 参照: UniProt: A6QP16, ubiquitinyl hydrolase 1 #3: 化合物 | ChemComp-ZN / |
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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: 3.69 Å3/Da / 溶媒含有率: 66.68 % |
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結晶化 | 温度: 285 K / pH: 6.5 詳細: 100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-データ収集
回折 | 平均測定温度: 285 K |
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放射光源 | 由来: シンクロトロン / サイト: Diamond / ビームライン: I04 / 波長: 0.9795 |
検出器 | タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年8月10日 / 詳細: COMPOUND REFRACTIVE LENSES |
放射 | モノクロメーター: DOUBLE CRYSTAL / 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: 0.9795 Å / 相対比: 1 |
反射 | 解像度: 3→76.1 Å / Num. obs: 17755 / % possible obs: 99 % / Observed criterion σ(I): -3 / 冗長度: 3.5 % / Biso Wilson estimate: 85.71 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.64 |
反射 シェル | 解像度: 3→3.1 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.4869 / Mean I/σ(I) obs: 2.05 / % possible all: 95.3 |
-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: 2WWZ, 1UBQ 解像度: 3.03→76.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 22.303 / SU ML: 0.382 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.866 / ESU R Free: 0.389 / 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: 81.9 Å2
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精密化ステップ | サイクル: LAST / 解像度: 3.03→76.1 Å
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拘束条件 |
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