+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1or3 | ||||||
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タイトル | APOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165 | ||||||
要素 | PROTEIN (APOLIPOPROTEIN E) | ||||||
キーワード | LIPID BINDING PROTEIN / 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 / 多波長異常分散 / 解像度: 1.73 Å | ||||||
データ登録者 | Rupp, B. / Segelke, B.W. | ||||||
引用 | ジャーナル: Protein Sci. / 年: 2000 タイトル: Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding. 著者: Segelke, B.W. / Forstner, M. / Knapp, M. / Trakhanov, S.D. / Parkin, S. / Newhouse, Y.M. / Bellamy, H.D. / Weisgraber, K.H. / Rupp, B. | ||||||
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 | 1or3.cif.gz | 43.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1or3.ent.gz | 31.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1or3.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/or/1or3 ftp://data.pdbj.org/pub/pdb/validation_reports/or/1or3 | 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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 19297.805 Da / 分子数: 1 / 断片: RECEPTOR BINDING DOMAIN / 由来タイプ: 組換発現 詳細: SELENOMETHIONINE MUTANT USED IN MAD PHASING EXPERIMENT 由来: (組換発現) Homo sapiens (ヒト) / 株: BL21, B834(DE)MET- / プラスミド: PET / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21, B834(DE)MET- / 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: 1.76 Å3/Da / 溶媒含有率: 30 % / 解説: 4 WAVELENGTHS USED FOR PHASING (ALS BEAMLINE 5.0.2) | ||||||||||||||||||||||||||||||
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結晶化 | pH: 5.6 詳細: RT, 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400, 1% 2-ME. NOTE: W/O 2-ME OR HIGHER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR2). | ||||||||||||||||||||||||||||||
溶液の組成 |
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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 | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 125 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.5418 |
検出器 | タイプ: ADSC / 検出器: AREA DETECTOR / 日付: 1997年5月15日 / 詳細: COLLIMATOR |
放射 | モノクロメーター: GRAPHITE / 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.73→25 Å / Num. obs: 16782 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / 冗長度: 2.9 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 6.8 / Net I/σ(I): 27.4 |
反射 シェル | 解像度: 1.73→1.86 Å / 冗長度: 2.8 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3.7 / Rsym value: 22.5 / % possible all: 95.7 |
反射 | *PLUS Num. measured all: 48854 |
反射 シェル | *PLUS % possible obs: 89.9 % |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 1.73→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2 / 詳細: BULK SOLVENT MODEL USED
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原子変位パラメータ | Biso mean: 53.7 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.73→10 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.73→1.79 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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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: 3.851 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 53.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.358 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.33 |