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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: 1f5y | ||||||
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タイトル | NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BINDING MODULES OF THE HUMAN LDL RECEPTOR | ||||||
![]() | LOW-DENSITY LIPOPROTEIN RECEPTOR | ||||||
![]() | LIPID BINDING PROTEIN / Beta hairpin / 3-10 helix / calcium binding | ||||||
機能・相同性 | ![]() receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance ...receptor-mediated endocytosis involved in cholesterol transport / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / negative regulation of astrocyte activation / negative regulation of microglial cell activation / very-low-density lipoprotein particle receptor activity / PCSK9-LDLR complex / cholesterol import / low-density lipoprotein particle clearance / positive regulation of triglyceride biosynthetic process / clathrin heavy chain binding / negative regulation of receptor recycling / intestinal cholesterol absorption / low-density lipoprotein particle receptor activity / Chylomicron clearance / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / response to caloric restriction / LDL clearance / high-density lipoprotein particle clearance / regulation of protein metabolic process / lipoprotein catabolic process / phospholipid transport / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle / cholesterol transport / endolysosome membrane / cellular response to fatty acid / negative regulation of amyloid fibril formation / regulation of cholesterol metabolic process / negative regulation of protein metabolic process / artery morphogenesis / sorting endosome / amyloid-beta clearance / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / retinoid metabolic process / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / endocytosis / positive regulation of inflammatory response / apical part of cell / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / amyloid-beta binding / virus receptor activity / protease binding / basolateral plasma membrane / molecular adaptor activity / early endosome / lysosome / receptor complex / endosome membrane / external side of plasma membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / calcium ion binding / positive regulation of gene expression / cell surface / Golgi apparatus / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | 溶液NMR / Torsion angle dynamics (DYANA), simulated annealing, molecular dynamics (X-PLOR) for calcium coordination | ||||||
![]() | Kurniawan, N.D. / Atkins, A.R. / Brereton, I.M. / Kroon, P.A. / Smith, R. | ||||||
![]() | ![]() タイトル: NMR structure of a concatemer of the first and second ligand-binding modules of the human low-density lipoprotein receptor. 著者: Kurniawan, N.D. / Atkins, A.R. / Bieri, S. / Brown, C.J. / Brereton, I.M. / Kroon, P.A. / Smith, R. #1: ![]() タイトル: Calcium is Essential for the Structural Integrity of the Cysteine-Rich, Ligand-Binding Repeat of the Low-Density Lipoprotein Receptor 著者: Atkins, A.R. / Brereton, I.M. / Kroon, P.A. / Lee, H.T. / Smith, R. #2: ![]() タイトル: Folding, Calcium Binding, and Structural Characterization of a Concatemer of the First and Second Ligand-Binding Modules of the Low-Density Lipoprotein Receptor 著者: Bieri, S. / Atkins, A.R. / Lee, H.T. / Winzor, D.J. / Smith, R. / Kroon, P.A. #3: ![]() タイトル: Three-Dimensional Structure of a Cysteine-Rich Repeat from the Low-Density Lipoprotein Receptor 著者: Daly, N.L. / Scanlon, M.J. / Djordjevic, J.T. / Kroon, P.A. / Smith, R. #4: ![]() タイトル: Three-Dimensional Structure of the Second Cysteine-Rich Repeat from the Human Low-Density Lipoprotein Receptor 著者: Daly, N.L. / Djordjevic, J.T. / Kroon, P.A. / Smith, R. | ||||||
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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 | ![]() | 471.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 393.5 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 356.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 483.9 KB | 表示 | |
XML形式データ | ![]() | 30 KB | 表示 | |
CIF形式データ | ![]() | 50.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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NMR アンサンブル |
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要素
#1: タンパク質 | 分子量: 9258.997 Da / 分子数: 1 / 断片: LIGAND-BINDING MODULES 1-2 / 由来タイプ: 組換発現 / 詳細: LIGAND-BINDING MODULE CONCATEMER / 由来: (組換発現) ![]() ![]() ![]() | ||
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#2: 化合物 | Has protein modification | Y | |
-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||||||
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NMR実験 |
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NMR実験の詳細 | Text: This structure was determined using standard 2D homonuclear techniques |
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試料調製
詳細 |
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試料状態 | イオン強度: 0.045 / pH: 5.5 / 圧: atmospheric atm / 温度: 310 K | |||||||||
結晶化 | *PLUS 手法: other / 詳細: NMR |
-NMR測定
NMRスペクトロメーター | タイプ: Bruker DMX / 製造業者: Bruker / モデル: DMX / 磁場強度: 750 MHz |
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解析
NMR software |
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精密化 | 手法: Torsion angle dynamics (DYANA), simulated annealing, molecular dynamics (X-PLOR) for calcium coordination ソフトェア番号: 1 詳細: NMR inputs: NOE total 889: 286 intra, 273 sequential, 184 medium, 146 long range; Others: 32 dihedral restraints, 13 h-bonds, 12 calcium coordination | ||||||||||||||||||||||||
代表構造 | 選択基準: lowest energy | ||||||||||||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 50 / 登録したコンフォーマーの数: 20 |