+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1av1 | ||||||
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タイトル | CRYSTAL STRUCTURE OF HUMAN APOLIPOPROTEIN A-I | ||||||
要素 | APOLIPOPROTEIN A-IApolipoprotein AI | ||||||
キーワード | LIPID TRANSPORT / LIPOPROTEIN (リポタンパク質) / CHOLESTEROL METABOLISM / ATHEROSCLEROSIS (アテローム性動脈硬化) / HDL / LCAT-ACTIVATION | ||||||
機能・相同性 | 機能・相同性情報 Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport ...Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport / cholesterol import / high-density lipoprotein particle binding / ABC transporters in lipid homeostasis / blood vessel endothelial cell migration / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / peptidyl-methionine modification / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / phosphatidylcholine metabolic process / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / lipid storage / Chylomicron assembly / positive regulation of cholesterol metabolic process / phospholipid homeostasis / high-density lipoprotein particle clearance / high-density lipoprotein particle remodeling / phospholipid efflux / chemorepellent activity / cholesterol transfer activity / reverse cholesterol transport / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / cholesterol transport / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / high-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / endothelial cell proliferation / negative regulation of interleukin-1 beta production / Scavenging by Class A Receptors / cholesterol efflux / cholesterol binding / negative chemotaxis / adrenal gland development / positive regulation of Rho protein signal transduction / cholesterol biosynthetic process / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cholesterol efflux / Scavenging of heme from plasma / positive regulation of phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / Retinoid metabolism and transport / positive regulation of stress fiber assembly / endocytic vesicle lumen / heat shock protein binding / cholesterol metabolic process / cholesterol homeostasis / integrin-mediated signaling pathway / Post-translational protein phosphorylation / regulation of protein phosphorylation / Heme signaling / phospholipid binding / PPARA activates gene expression / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / Platelet degranulation / amyloid-beta binding / cytoplasmic vesicle / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / エンドソーム / protein stabilization / G protein-coupled receptor signaling pathway / Amyloid fiber formation / 小胞体 / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / 細胞膜 / 細胞質基質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 多重同系置換・異常分散 / 解像度: 4 Å | ||||||
データ登録者 | Borhani, D.W. / Rogers, D.P. / Engler, J.A. / Brouillette, C.G. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1997 タイトル: Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation. 著者: Borhani, D.W. / Rogers, D.P. / Engler, J.A. / Brouillette, C.G. #1: ジャーナル: Biochemistry / 年: 1997 タイトル: Structural Analysis of Apolipoprotein A-I: Limited Proteolysis of Methionine-Reduced and-Oxidized Lipid-Free and Lipid-Bound Human Apo A-I 著者: Roberts, L.M. / Ray, M.J. / Shih, T.W. / Hayden, E. / Reader, M.M. / Brouillette, C.G. #2: ジャーナル: Biochemistry / 年: 1997 タイトル: Truncation of the Amino Terminus of Human Apolipoprotein A-I Substantially Alters Only the Lipid-Free Conformation 著者: Rogers, D.P. / Brouillette, C.G. / Engler, J.A. / Tendian, S.W. / Roberts, L. / Mishra, V.K. / Anantharamaiah, G.M. / Lund-Katz, S. / Phillips, M.C. / Ray, M.J. #3: ジャーナル: Biochim.Biophys.Acta / 年: 1995 タイトル: Structural Models of Human Apolipoprotein A-I 著者: Brouillette, C.G. / Anantharamaiah, G.M. | ||||||
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 | 1av1.cif.gz | 147 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1av1.ent.gz | 117.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1av1.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/av/1av1 ftp://data.pdbj.org/pub/pdb/validation_reports/av/1av1 | HTTPS FTP |
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-関連構造データ
類似構造データ |
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-リンク
-集合体
登録構造単位 |
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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-要素
#1: タンパク質 | 分子量: 23440.559 Da / 分子数: 4 / 断片: LIPID-BINDING DOMAIN / 変異: N-TERMINAL MET, DEL(1-43) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 組織: BLOOD血液 / 細胞株: BL21 / プラスミド: BL21 / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P02647 |
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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: 2 |
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-試料調製
結晶 | マシュー密度: 5.83 Å3/Da / 溶媒含有率: 72 % 解説: DATA WERE EXCLUDED ON A RESOLUTION-DEPENDENT BASIS FOR ALL RESOLUTION SHELLS IN WHICH THE FOR FULLY-RECORDED REFLECTIONS IN THAT SHELL WAS LESS THAN 2.5. 結晶化 | 温度: 277 K / pH: 7.5 | 詳細: PROTEIN WAS CRYSTALLIZED FROM 1.2 M NA CITRATE, 100 MM HEPES, PH 7.5 AT 4 DEGREES CELSIUS. CRYSTALS WERE STABILIZED IN 1.4 M NA CITRATE, 100 MM HEPES, PH 7.5., temperature 277K 結晶化 | *PLUS 温度: 4 ℃ / 手法: unknown / PH range low: 7.5 / PH range high: 6.5 溶液の組成 | *PLUS 濃度: 1.2 M / 一般名: sodium citrate |
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-データ収集
回折 | 平均測定温度: 283 K |
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放射光源 | 由来: 回転陽極 / タイプ: MACSCIENCE / 波長: 1.5418 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1996年1月24日 / 詳細: DUAL SLITS |
放射 | モノクロメーター: GRAPHITE(002) / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 4→30 Å / Num. obs: 16089 / % possible obs: 85 % / Observed criterion σ(I): 0 / 冗長度: 3.6 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.166 / Net I/σ(I): 3.7 |
反射 シェル | 解像度: 4→4.22 Å / 冗長度: 1.3 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 0.9 / Rsym value: 0.732 / % possible all: 50 |
反射 シェル | *PLUS % possible obs: 50 % |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 多重同系置換・異常分散 / 解像度: 4→27 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: 24 (GROUPED) THERMAL FACT / 交差検証法: THROUGHOUT / σ(F): 2 詳細: DATA USED IN REFINEMENT WERE SHARPENED BY APPLICATION OF AN ARTIFICIAL TEMPERATURE FACTOR (-70. A**2).
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原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 4→27 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 4→4.18 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 8
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Xplor file |
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.843 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rwork: 0.43 |