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基本情報
登録情報 | データベース: PDB / ID: 8eoj | ||||||
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タイトル | Microsomal triglyceride transfer protein | ||||||
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![]() | TRANSPORT PROTEIN / Microsomal triglyceride transfer protein / human liver / LIPID TRANSPORT / ISOMERASE | ||||||
機能・相同性 | ![]() plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / phosphatidylcholine transfer activity / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / triglyceride transport / interleukin-23-mediated signaling pathway ...plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / phosphatidylcholine transfer activity / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / triglyceride transport / interleukin-23-mediated signaling pathway / phosphatidylethanolamine transfer activity / phospholipid transfer activity / LDL remodeling / procollagen-proline 4-dioxygenase activity / thiol oxidase activity / protein disulfide-isomerase / ceramide 1-phosphate transfer activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / very-low-density lipoprotein particle assembly / phospholipid transporter activity / endoplasmic reticulum chaperone complex / Collagen biosynthesis and modifying enzymes / protein folding in endoplasmic reticulum / lipid transporter activity / Chylomicron assembly / lipoprotein metabolic process / phospholipid transport / cholesterol transfer activity / Interleukin-23 signaling / low-density lipoprotein particle remodeling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / lipoprotein transport / microvillus membrane / triglyceride metabolic process / protein disulfide isomerase activity / Insulin processing / Detoxification of Reactive Oxygen Species / apolipoprotein binding / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of cell adhesion / protein secretion / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / establishment of localization in cell / cholesterol homeostasis / Hedgehog ligand biogenesis / brush border membrane / Post-translational protein phosphorylation / lipid metabolic process / response to calcium ion / circadian rhythm / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / basolateral plasma membrane / vesicle / positive regulation of viral entry into host cell / cytoskeleton / receptor complex / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / lipid binding / protein-containing complex binding / Golgi apparatus / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.07 Å | ||||||
![]() | Zhang, Z. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: High-resolution structural-omics of human liver enzymes. 著者: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu / ![]() 要旨: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level. | ||||||
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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PDBx/mmCIF形式 | ![]() | 244.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 191.2 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.4 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.4 MB | 表示 | |
XML形式データ | ![]() | 48.6 KB | 表示 | |
CIF形式データ | ![]() | 71.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 23426 ![]() 28377MC ![]() 7uzmC ![]() 8ekwC ![]() 8ekyC ![]() 8em2C ![]() 8emrC ![]() 8emsC ![]() 8emtC ![]() 8eneC ![]() 8eorC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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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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要素
#1: タンパク質 | 分子量: 57190.137 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#2: タンパク質 | 分子量: 99474.102 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 | 名称: Microsomal triglyceride transfer protein / タイプ: COMPLEX / Entity ID: all / 由来: NATURAL |
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由来(天然) | 生物種: ![]() |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 3291 nm / 最小 デフォーカス(公称値): 170 nm |
撮影 | 電子線照射量: 41.25 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 487553 | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.07 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 249877 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 72.46 Å2 | ||||||||||||||||||||||||
拘束条件 |
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