+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 9fj3 | |||||||||
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タイトル | Structure of ubiquitin bound of coiled-coil UIM form 2 | |||||||||
要素 |
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キーワード | SIGNALING PROTEIN / Ubiquitin / coiled-coil peptide / UIM | |||||||||
機能・相同性 | 機能・相同性情報 Maturation of protein E / 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 ...Maturation of protein E / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Endosomal Sorting Complex Required For Transport (ESCRT) / 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 / 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 / VLDLR internalisation and degradation / 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 / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / PINK1-PRKN Mediated Mitophagy / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / SCF-beta-TrCP mediated degradation of Emi1 / 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 / 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 / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Degradation of AXIN / Peroxisomal protein import / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR2 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Stabilization of p53 / EGFR downregulation / Hedgehog ligand biogenesis / Negative regulation of FGFR4 signaling / Defective CFTR causes cystic fibrosis / Termination of translesion DNA synthesis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Negative regulation of FGFR1 signaling 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) synthetic construct (人工物) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.4 Å | |||||||||
データ登録者 | Paredes Vergara, P. / Huang, D.T. | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Chem Sci / 年: 2024 タイトル: An engineered ubiquitin binding coiled coil peptide. 著者: Vosbein, P. / Vergara, P.P. / Huang, D.T. / Thomson, A.R. | |||||||||
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 | 9fj3.cif.gz | 111.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb9fj3.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 9fj3.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 | 9fj3_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 9fj3_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | 9fj3_validation.xml.gz | 15.3 KB | 表示 | |
CIF形式データ | 9fj3_validation.cif.gz | 20.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fj/9fj3 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/9fj3 | HTTPS FTP |
-関連構造データ
類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
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-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: 8922.141 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Contain GSGGS at the N-terminus resulted from cloning and cleavage of tag. C-terminal RGG are not modeled due to the absence of electron density 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 #2: タンパク質・ペプチド | 分子量: 2299.524 Da / 分子数: 2 / 由来タイプ: 合成 詳細: Synthetic coiled-coil peptide. N-terminus of Chains B and E are covalently linked to the N-terminus of Chains C and F, respectively, by a triazole crosslinker (A1IDH). 由来: (合成) synthetic construct (人工物) #3: タンパク質・ペプチド | 分子量: 2247.806 Da / 分子数: 2 / 由来タイプ: 合成 詳細: Synthetic coiled-coil peptide. N-terminus of Chain C is covalently linked to the N-terminus of Chain B by a triazole crosslinker (A1IDH). C-terminal QG are not modeled due to absence of electron density. 由来: (合成) synthetic construct (人工物) #4: 化合物 | 分子量: 199.164 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C7H9N3O4 / タイプ: SUBJECT OF INVESTIGATION #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
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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: 2.02 Å3/Da / 溶媒含有率: 39.12 % |
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結晶化 | 温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 0.1 M amino acids, 0.1 M buffer system 1, pH 6.6-6.7 and 36-38 %(v/v) precipitant mix 1 (Molecular Dimension) |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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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: 0.95374 Å |
検出器 | タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2023年8月2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: 0.95374 Å / 相対比: 1 |
反射 | 解像度: 1.4→41.63 Å / Num. obs: 58645 / % possible obs: 97 % / 冗長度: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 10.5 |
反射 シェル | 解像度: 1.4→1.44 Å / Num. unique obs: 3872 / CC1/2: 0.781 |
-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 / 解像度: 1.4→41.63 Å / SU ML: 0.18 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 33.89 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.4→41.63 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Origin x: -42.0029 Å / Origin y: -41.6726 Å / Origin z: -14.3957 Å
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精密化 TLSグループ | Selection details: all |