+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1nfo | ||||||
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タイトル | APOLIPOPROTEIN E2 (APOE2, D154A MUTATION) | ||||||
要素 | APOLIPOPROTEIN E2 | ||||||
キーワード | LIPID TRANSPORT / HEPARIN-BINDING / PLASMA PROTEIN / HDL / VLDL | ||||||
機能・相同性 | 機能・相同性情報 chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle ...chylomicron remnant / lipid transport involved in lipid storage / triglyceride-rich lipoprotein particle clearance / intermediate-density lipoprotein particle clearance / positive regulation of lipid transport across blood-brain barrier / positive regulation of heparan sulfate proteoglycan binding / regulation of cellular response to very-low-density lipoprotein particle stimulus / metal chelating activity / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / lipoprotein particle / regulation of amyloid-beta clearance / discoidal high-density lipoprotein particle / intermediate-density lipoprotein particle / chylomicron remnant clearance / maintenance of location in cell / very-low-density lipoprotein particle clearance / very-low-density lipoprotein particle remodeling / Chylomicron clearance / negative regulation of triglyceride metabolic process / response to caloric restriction / acylglycerol homeostasis / NMDA glutamate receptor clustering / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of cholesterol metabolic process / regulation of behavioral fear response / regulation of amyloid fibril formation / regulation of protein metabolic process / high-density lipoprotein particle clearance / multivesicular body, internal vesicle / lipoprotein catabolic process / melanosome organization / lipid transporter activity / chylomicron / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle receptor binding / phospholipid efflux / AMPA glutamate receptor clustering / cholesterol transfer activity / positive regulation by host of viral process / reverse cholesterol transport / very-low-density lipoprotein particle / positive regulation of amyloid-beta clearance / high-density lipoprotein particle assembly / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / protein import / negative regulation of blood coagulation / high-density lipoprotein particle / low-density lipoprotein particle remodeling / negative regulation of amyloid fibril formation / heparan sulfate proteoglycan binding / synaptic transmission, cholinergic / negative regulation of cholesterol biosynthetic process / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / amyloid precursor protein metabolic process / regulation of amyloid precursor protein catabolic process / positive regulation of membrane protein ectodomain proteolysis / negative regulation of protein metabolic process / HDL remodeling / negative regulation of endothelial cell migration / Scavenging by Class A Receptors / artery morphogenesis / cholesterol efflux / regulation of axon extension / regulation of cholesterol metabolic process / triglyceride metabolic process / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / positive regulation of dendritic spine development / regulation of innate immune response / virion assembly / locomotory exploration behavior / negative regulation of amyloid-beta formation / negative regulation of endothelial cell proliferation / regulation of neuronal synaptic plasticity / positive regulation of endocytosis / lipoprotein particle binding / antioxidant activity / response to dietary excess / negative regulation of blood vessel endothelial cell migration / negative regulation of long-term synaptic potentiation / positive regulation of dendritic spine maintenance / negative regulation of platelet activation / intracellular transport / positive regulation of cholesterol efflux / regulation of protein-containing complex assembly / negative regulation of protein secretion / fatty acid homeostasis / cholesterol catabolic process / long-term memory / long-chain fatty acid transport / positive regulation of lipid biosynthetic process / regulation of proteasomal protein catabolic process / synaptic cleft 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2 Å | ||||||
データ登録者 | Rupp, B. / Parkin, S. | ||||||
引用 | ジャーナル: Nat.Struct.Biol. / 年: 1996 タイトル: Novel mechanism for defective receptor binding of apolipoprotein E2 in type III hyperlipoproteinemia. 著者: Dong, L.M. / Parkin, S. / Trakhanov, S.D. / Rupp, B. / Simmons, T. / Arnold, K.S. / Newhouse, Y.M. / Innerarity, T.L. / Weisgraber, K.H. | ||||||
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 | 1nfo.cif.gz | 41.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1nfo.ent.gz | 29.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1nfo.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/nf/1nfo ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nfo | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 22064.021 Da / 分子数: 1 / 断片: 22KD RECEPTOR BINDING DOMAIN / 変異: D154A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: E2 / 器官: PLASMA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02649 |
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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: 3.07 Å3/Da / 溶媒含有率: 59.9 % | ||||||||||||||||||||||||||||||
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結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Wilson, C., (1991) Science, 252, 1817. / PH range low: 5.3 / PH range high: 4.5 | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 130 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RUH2R / 波長: 1.5418 |
検出器 | タイプ: ADSC / 検出器: AREA DETECTOR |
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: 2→15 Å / % possible obs: 94.2 % / 冗長度: 3.5 % / Rmerge(I) obs: 0.0509 |
反射 | *PLUS Num. obs: 8964 / Observed criterion σ(I): 2 |
-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: PHASING MODEL DERIVED FROM 1NFN 解像度: 2→8 Å / Num. parameters: 5267 / Num. restraintsaints: 4789 / 交差検証法: R-FREE / σ(F): 0 詳細: RESIDUES 23 AND 24 ARE NOT WELL DEFINED AND THE BOND ANGLES ARE ON THE BORDERLINE OF THE ALLOWED REGIONS. CONSIDERING THE WEAK ELECTRON DENSITY THERE IS NO POINT IN ATTEMPTING TO ACCURATELY ...詳細: RESIDUES 23 AND 24 ARE NOT WELL DEFINED AND THE BOND ANGLES ARE ON THE BORDERLINE OF THE ALLOWED REGIONS. CONSIDERING THE WEAK ELECTRON DENSITY THERE IS NO POINT IN ATTEMPTING TO ACCURATELY REFINE THESE TWO RESIDUES.
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溶媒の処理 | 溶媒モデル: 'SWAT' IN SHELXL93 | |||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2→8 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: SHELXL-93 / 分類: refinement | |||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor Rfree: 0.27 | |||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |