+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3r2p | ||||||
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タイトル | 2.2 Angstrom Crystal Structure of C Terminal Truncated Human Apolipoprotein A-I Reveals the Assembly of HDL by Dimerization. | ||||||
要素 | Apolipoprotein A-IApolipoprotein AI | ||||||
キーワード | LIPID TRANSPORT / amphipathic alpha-helix / major protein of high density lipoprotein (HDL) / lipid binding (脂質) / plasma | ||||||
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 / シンクロトロン / 分子置換 / 解像度: 2.2045 Å | ||||||
データ登録者 | Mei, X. / Atkinson, D. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2011 タイトル: Crystal Structure of C-terminal Truncated Apolipoprotein A-I Reveals the Assembly of High Density Lipoprotein (HDL) by Dimerization. 著者: Mei, X. / Atkinson, D. | ||||||
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 | 3r2p.cif.gz | 87.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3r2p.ent.gz | 67.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3r2p.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/r2/3r2p ftp://data.pdbj.org/pub/pdb/validation_reports/r2/3r2p | 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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詳細 | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x, -y, z and x, y+1, Z |
-要素
#1: タンパク質 | 分子量: 21656.234 Da / 分子数: 1 / 断片: N-terminal domain (UNP 25-208) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APOA1 / プラスミド: pDEST-His6-MBP / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) CodonPlus-RIL / 参照: UniProt: P02647 |
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#2: 水 | ChemComp-HOH / |
-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: 2.63 Å3/Da / 溶媒含有率: 53.16 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.6 詳細: 0.15M potassium bromide, 30% PEG 2000 MME, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: NSLS / ビームライン: X4C / 波長: 0.91994 Å |
検出器 | タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2010年4月15日 |
放射 | モノクロメーター: Si 111 channel / 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: 0.91994 Å / 相対比: 1 |
反射 | 解像度: 2.2→50 Å / Num. all: 11930 / Num. obs: 11930 / % possible obs: 98.2 % / Observed criterion σ(F): 2.95 / Observed criterion σ(I): 2.95 / 冗長度: 6.4 % / Biso Wilson estimate: 37.46 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.017 |
反射 シェル | 解像度: 2.2→2.24 Å / 冗長度: 4.2 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.95 / Num. unique all: 532 / % possible all: 89.4 |
-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 開始モデル: Use the Se-Met derivative to obtain the starting model from SAD experiment. 解像度: 2.2045→34.788 Å / SU ML: 0.33 / Isotropic thermal model: Mixed individual ADP with TLS / σ(F): 0 / 位相誤差: 33.52 / 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: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 47.738 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 63.7952 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.2045→34.788 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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