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データを開く
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基本情報
| 登録情報 | データベース: PDB / ID: 9e2u | |||||||||
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| タイトル | Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) | |||||||||
要素 |
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キーワード | LIGASE / CRBN / DDB1 / IKZF2 / ALV1 / DEGRADATION / E3 LIGASE / MOLECULAR GLUE | |||||||||
| 機能・相同性 | 機能・相同性情報negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex ...negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm 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: 4.11 Å | |||||||||
データ登録者 | Nowak, R.P. / Fischer, E.S. | |||||||||
| 資金援助 | 米国, 2件
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引用 | ジャーナル: Mol Cell / 年: 2025タイトル: Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation. 著者: Mikołaj Słabicki / Jiho Park / Radosław P Nowak / Shourya S Roy Burman / Jesse Pellman / Charles Zou / Hlib Razumkov / Jeannie Carreiro / Simran Rastogi / Anna Goldstein / Marek M Nagiec / ...著者: Mikołaj Słabicki / Jiho Park / Radosław P Nowak / Shourya S Roy Burman / Jesse Pellman / Charles Zou / Hlib Razumkov / Jeannie Carreiro / Simran Rastogi / Anna Goldstein / Marek M Nagiec / Katherine A Donovan / Jianwei Che / Moritz Hunkeler / Qixiang Geng / Chi-Lin Hsu / Megha Lakshminarayan / Chelsea Shu / Rebecca L Zon / Zuzanna Kozicka / Paul M C Park / Jonathan M Tsai / Hojong Yoon / Lyn H Jones / Adam S Sperling / Nathanael S Gray / Eric S Fischer / Benjamin L Ebert / ![]() 要旨: Glutarimide analogs, such as thalidomide, redirect the E3 ubiquitin ligase CRL4 to induce degradation of certain zinc finger (ZF) proteins. Although the core structural motif recognized by CRBN has ...Glutarimide analogs, such as thalidomide, redirect the E3 ubiquitin ligase CRL4 to induce degradation of certain zinc finger (ZF) proteins. Although the core structural motif recognized by CRBN has been characterized, it does not fully explain substrate specificity. To explore the role of residues adjacent to this core motif, we constructed a comprehensive ZF reporter library of 9,097 reporters derived from 1,655 human ZF proteins and conducted a library-on-library screen with 29 glutarimide analogs to identify compounds that collectively degrade 38 ZF reporters. Cryo-electron microscopy and crystal structures of ZFs in complex with CRBN revealed the importance of interactions beyond the core ZF degron. We used systematic mutagenesis of ZFs and CRBN to identify modes of neosubstrate recruitment requiring distinct amino acids. Finally, we found subtle chemical variations in glutarimide analogs that alter target scope and selectivity, thus providing a roadmap for their rational design. #1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019 タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. 著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() 要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
| 履歴 |
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構造の表示
| 構造ビューア | 分子: Molmil Jmol/JSmol |
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ダウンロードとリンク
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ダウンロード
| PDBx/mmCIF形式 | 9e2u.cif.gz | 4.8 MB | 表示 | PDBx/mmCIF形式 |
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| PDB形式 | pdb9e2u.ent.gz | 表示 | PDB形式 | |
| PDBx/mmJSON形式 | 9e2u.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 | 9e2u_validation.pdf.gz | 2 MB | 表示 | wwPDB検証レポート |
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| 文書・詳細版 | 9e2u_full_validation.pdf.gz | 2.1 MB | 表示 | |
| XML形式データ | 9e2u_validation.xml.gz | 382 KB | 表示 | |
| CIF形式データ | 9e2u_validation.cif.gz | 486.5 KB | 表示 | |
| アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/e2/9e2u ftp://data.pdbj.org/pub/pdb/validation_reports/e2/9e2u | HTTPS FTP |
-関連構造データ
| 関連構造データ | C: 同じ文献を引用 ( |
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| 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
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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: 96425.586 Da / 分子数: 8 断片: internal deletion of the BPB domain,internal deletion of the BPB domain 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DDB1, XAP1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q16531#2: タンパク質 | 分子量: 53005.207 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CRBN, AD-006 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q96SW2#3: タンパク質 | 分子量: 20272.938 Da / 分子数: 8 / 由来タイプ: 組換発現 詳細: MDWSHPQFEKSAVGLNDIFEAQKIEWHEGGGGSGENLYFQGG is the StrepII Avi TEV cleavable tag. Construct encompasses 3 ZnF domains. The C-terminal tail that is not visible 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IKZF2 / 発現宿主: Trichoplusia ni (イラクサキンウワバ)#4: 化合物 | ChemComp-RN9 / #5: 化合物 | ChemComp-ZN / 研究の焦点であるリガンドがあるか | Y | Has protein modification | N | |
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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: 3.07 Å3/Da / 溶媒含有率: 59.92 % |
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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 / 詳細: 20.455% PEG 3350, 0.214 M Li3 Cit |
-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: APS / ビームライン: 24-ID-E / 波長: 0.97918 Å |
| 検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年12月11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: 0.97918 Å / 相対比: 1 |
| 反射 | 解像度: 4.11→168.59 Å / Num. obs: 130289 / % possible obs: 100 % / 冗長度: 9.3 % / Biso Wilson estimate: 187.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.074 / Rrim(I) all: 0.165 / Net I/σ(I): 9.4 |
| 反射 シェル | 解像度: 4.11→4.18 Å / 冗長度: 9.8 % / Rmerge(I) obs: 2.569 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6391 / CC1/2: 0.37 / Rpim(I) all: 1.282 / Rrim(I) all: 2.878 / % possible all: 99.9 |
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解析
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| 精密化 | 構造決定の手法: 分子置換 / 解像度: 4.11→69.33 Å / SU ML: 0.6789 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.9451 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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| 溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 原子変位パラメータ | Biso mean: 213.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 精密化ステップ | サイクル: LAST / 解像度: 4.11→69.33 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: -116.907381677 Å / Origin y: 56.0573213676 Å / Origin z: -64.3177157953 Å
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| 精密化 TLSグループ | Selection details: all |
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コントローラー
万見について




Homo sapiens (ヒト)
X線回折
米国, 2件
引用



PDBj












Trichoplusia ni (イラクサキンウワバ)

