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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: 7zet | ||||||
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タイトル | Crystal structure of human Clusterin, crystal form I | ||||||
![]() | Clusterin | ||||||
![]() | CHAPERONE / molecular chaperone / complement system / Alzheimer's disease | ||||||
機能・相同性 | ![]() immune complex clearance / perinuclear endoplasmic reticulum lumen / regulation of neuronal signal transduction / positive regulation of neurofibrillary tangle assembly / : / central nervous system myelin maintenance / : / response to misfolded protein / negative regulation of response to endoplasmic reticulum stress / spherical high-density lipoprotein particle ...immune complex clearance / perinuclear endoplasmic reticulum lumen / regulation of neuronal signal transduction / positive regulation of neurofibrillary tangle assembly / : / central nervous system myelin maintenance / : / response to misfolded protein / negative regulation of response to endoplasmic reticulum stress / spherical high-density lipoprotein particle / protein carrier chaperone / Terminal pathway of complement / protein targeting to lysosome involved in chaperone-mediated autophagy / chromaffin granule / regulation of amyloid-beta clearance / microglial cell proliferation / misfolded protein binding / apical dendrite / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / reverse cholesterol transport / positive regulation of ubiquitin-dependent protein catabolic process / protein import / negative regulation of amyloid fibril formation / complement activation / neurofibrillary tangle / positive regulation of tau-protein kinase activity / Antimicrobial peptides / positive regulation of amyloid fibril formation / low-density lipoprotein particle receptor binding / positive regulation of amyloid-beta formation / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / chaperone-mediated protein complex assembly / negative regulation of protein-containing complex assembly / chaperone-mediated protein folding / positive regulation of intrinsic apoptotic signaling pathway / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / platelet alpha granule lumen / complement activation, classical pathway / Regulation of Complement cascade / microglial cell activation / positive regulation of protein-containing complex assembly / response to virus / tau protein binding / cell morphogenesis / lipid metabolic process / positive regulation of receptor-mediated endocytosis / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of cell population proliferation / protein-folding chaperone binding / regulation of apoptotic process / collagen-containing extracellular matrix / negative regulation of neuron apoptotic process / mitochondrial inner membrane / protein stabilization / blood microparticle / positive regulation of apoptotic process / protein heterodimerization activity / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / ubiquitin protein ligase binding / synapse / protein-containing complex binding / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Yuste-Checa, P. / Bracher, A. / Hartl, F.U. | ||||||
資金援助 | 1件
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![]() | ![]() タイトル: Crystal structure of human Clusterin, crystal form I 著者: Yuste-Checa, P. / Bracher, A. / Hartl, F.U. | ||||||
履歴 |
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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 | ![]() | 95.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 69.5 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 947.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 949.7 KB | 表示 | |
XML形式データ | ![]() | 15 KB | 表示 | |
CIF形式データ | ![]() | 19.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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1 |
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2 |
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単位格子 |
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要素
#1: タンパク質 | 分子量: 47038.852 Da / 分子数: 1 / 断片: Clu-delta(214-238) / 変異: deletion(214-238) / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() | ||
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#2: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
#3: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
#4: 糖 | ChemComp-NAG / 研究の焦点であるリガンドがあるか | N | |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 3 Å3/Da / 溶媒含有率: 59.07 % / Mosaicity: 0.25 ° |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.6 詳細: 30% PEG-4000, 0.2 M NH4-acetate, 0.1 M Na-citrate pH 5.6 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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放射光源 | 由来: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年12月2日 | ||||||||||||||||||||||||||||||
放射 | 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: 0.7749 Å / 相対比: 1 | ||||||||||||||||||||||||||||||
反射 | 解像度: 2.8→49.08 Å / Num. obs: 13861 / % possible obs: 98.2 % / 冗長度: 3.7 % / Biso Wilson estimate: 75.02 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.088 / Rrim(I) all: 0.172 / Net I/σ(I): 5.9 / Num. measured all: 50668 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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-位相決定
位相決定 | 手法: ![]() | ||||||
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Phasing MR | R rigid body: 0.596
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解析
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精密化 | 構造決定の手法: ![]() 開始モデル: AlphaFold AF-P10909-F1-model_v1.pdb 解像度: 2.8→27.61 Å / SU ML: 0.54 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 35.41 / 立体化学のターゲット値: ML 詳細: The Clusterin construct is a glyco-protein, which was expressed in the presence of the alpha-mannosidase I inhibitor kifunensine, which prevents trimming of mannose moieties, resulting in ...詳細: The Clusterin construct is a glyco-protein, which was expressed in the presence of the alpha-mannosidase I inhibitor kifunensine, which prevents trimming of mannose moieties, resulting in oligo-mannose N-glycans, and thereby prevents processing to mature complex N-glycans (Chang et al., Structure 15, 267(2007), Fig. 1B). Asn residues 86, 103, 145, 291, 354 and 374 are expected to carry predominantly NAG-NAG-BMA-(3->1)MAN-MAN-MAN (6->1)-MAN (3->1)MAN-MAN (6->1)MAN-MAN N-glycan trees (Chang et al., Structure 15, 267(2007), Fig. 1B).
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 161.13 Å2 / Biso mean: 80.9892 Å2 / Biso min: 36.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 2.8→27.61 Å
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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