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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: 8ruu | ||||||
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タイトル | Fabs derived from bimekizumab in complex with IL-17F | ||||||
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![]() | IMMUNOSUPPRESSANT / Complex Fab bimekizumab IL-17F / IL-17A / BKZ / IMMUNE SYSTEM | ||||||
機能・相同性 | ![]() regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / cytokine receptor binding ...regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / regulation of transforming growth factor beta receptor signaling pathway / cytokine receptor binding / positive regulation of cytokine production involved in inflammatory response / cartilage development / regulation of interleukin-6 production / cytokine binding / negative regulation of angiogenesis / positive regulation of cytokine production / cytokine activity / positive regulation of interleukin-6 production / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / protein heterodimerization activity / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Adams, R. / Lawson, A.D.G. | ||||||
資金援助 | 1件
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![]() | ![]() タイトル: Crystal Structure of Bimekizumab Fab Fragment in Complex with IL-17F Provides Molecular Basis for Dual IL-17A and IL-17F Inhibition. 著者: Adams, R. / Bunick, C.G. / Lawson, A.D.G. / Gomez, B. / Shaw, S. #1: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2012 タイトル: Towards automated crystallographic structure refinement with phenix.refine. 著者: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: 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: ![]() ![]() |
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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 | ![]() | 428.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 327.4 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 821 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 828.8 KB | 表示 | |
XML形式データ | ![]() | 36.6 KB | 表示 | |
CIF形式データ | ![]() | 50.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 1jpyS S: 精密化の開始モデル |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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: 抗体 | 分子量: 24522.445 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() #2: 抗体 | 分子量: 23635.279 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() #3: タンパク質 | 分子量: 14922.104 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q96PD4 #4: 多糖 | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | タイプ: oligosaccharide / 分子量: 894.823 Da / 分子数: 1 / 由来タイプ: 組換発現 #5: 糖 | ChemComp-NAG / | 研究の焦点であるリガンドがあるか | N | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 3.95 Å3/Da / 溶媒含有率: 68.9 % |
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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: PEG 8000, lithium sulphate, glycerol |
-データ収集
回折 | 平均測定温度: 193 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2014年11月28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: 0.976 Å / 相対比: 1 |
反射 | 解像度: 2.81→81.95 Å / Num. obs: 50718 / % possible obs: 99.9 % / 冗長度: 6.5 % / Biso Wilson estimate: 79.78 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 23.2 |
反射 シェル | 解像度: 2.81→2.88 Å / 冗長度: 6.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 25323 / Rpim(I) all: 0.258 / Rrim(I) all: 0.68 / % possible all: 99.9 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 1JPY 解像度: 2.81→81.95 Å / SU ML: 0.3981 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 26.1497 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: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 85.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.81→81.95 Å
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LS精密化 シェル |
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