+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2677 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Three-dimensional structure of human gamma-secretase at 4.5 angstrom resolution | |||||||||
マップデータ | Reconstruction of human gamma-secretase. The particles were selected by one-step of 3D classification. This map has good density for Nicastrin extracellular domain, but slightly worse density for transmembrane domain. | |||||||||
試料 |
| |||||||||
キーワード | human gamma-secretase / cryo EM | |||||||||
機能・相同性 | 機能・相同性情報 Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / amyloid precursor protein biosynthetic process / positive regulation of coagulation / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / protein catabolic process at postsynapse / positive regulation of amyloid precursor protein biosynthetic process ...Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / amyloid precursor protein biosynthetic process / positive regulation of coagulation / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / protein catabolic process at postsynapse / positive regulation of amyloid precursor protein biosynthetic process / positive regulation of endopeptidase activity / TGFBR3 PTM regulation / Noncanonical activation of NOTCH3 / sequestering of calcium ion / Notch receptor processing / central nervous system myelination / synaptic vesicle targeting / negative regulation of axonogenesis / membrane protein intracellular domain proteolysis / regulation of resting membrane potential / choline transport / T cell activation involved in immune response / skin morphogenesis / NOTCH4 Activation and Transmission of Signal to the Nucleus / growth factor receptor binding / regulation of synaptic vesicle cycle / dorsal/ventral neural tube patterning / myeloid dendritic cell differentiation / neural retina development / L-glutamate import across plasma membrane / Regulated proteolysis of p75NTR / regulation of phosphorylation / metanephros development / endoplasmic reticulum calcium ion homeostasis / locomotion / brain morphogenesis / nuclear outer membrane / amyloid precursor protein metabolic process / glutamate receptor signaling pathway / smooth endoplasmic reticulum calcium ion homeostasis / regulation of canonical Wnt signaling pathway / astrocyte activation involved in immune response / regulation of long-term synaptic potentiation / embryonic limb morphogenesis / aggresome / cell fate specification / skeletal system morphogenesis / ciliary rootlet / myeloid cell homeostasis / azurophil granule membrane / regulation of postsynapse organization / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; アスパラギン酸プロテアーゼ / G protein-coupled dopamine receptor signaling pathway / Golgi cisterna membrane / positive regulation of amyloid fibril formation / mitochondrial transport / adult behavior / positive regulation of dendritic spine development / positive regulation of receptor recycling / blood vessel development / regulation of neuron projection development / heart looping / protein glycosylation / amyloid precursor protein catabolic process / cerebral cortex cell migration / amyloid-beta formation / negative regulation of apoptotic signaling pathway / membrane protein ectodomain proteolysis / autophagosome assembly / endopeptidase activator activity / EPH-ephrin mediated repulsion of cells / smooth endoplasmic reticulum / hematopoietic progenitor cell differentiation / neuron development / somitogenesis / negative regulation of ubiquitin-dependent protein catabolic process / calcium ion homeostasis / T cell proliferation / Nuclear signaling by ERBB4 / rough endoplasmic reticulum / Notch signaling pathway / regulation of synaptic transmission, glutamatergic / neuron projection maintenance / Degradation of the extracellular matrix / NOTCH2 Activation and Transmission of Signal to the Nucleus / cellular response to calcium ion / positive regulation of glycolytic process / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / cerebellum development / post-embryonic development / epithelial cell proliferation / thymus development / negative regulation of protein phosphorylation / dendritic shaft / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / PDZ domain binding / apoptotic signaling pathway / synapse organization 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / ネガティブ染色法 / 解像度: 4.5 Å | |||||||||
データ登録者 | Lu PL / Bai XC / Ma D / Xie T / Yan CY / Sun LF / Yang GH / Zhao YY / Zhou R / Scheres SHW / Shi YG | |||||||||
引用 | ジャーナル: Nature / 年: 2014 タイトル: Three-dimensional structure of human γ-secretase. 著者: Peilong Lu / Xiao-Chen Bai / Dan Ma / Tian Xie / Chuangye Yan / Linfeng Sun / Guanghui Yang / Yanyu Zhao / Rui Zhou / Sjors H W Scheres / Yigong Shi / 要旨: The γ-secretase complex, comprising presenilin 1 (PS1), PEN-2, APH-1 and nicastrin, is a membrane-embedded protease that controls a number of important cellular functions through substrate cleavage. ...The γ-secretase complex, comprising presenilin 1 (PS1), PEN-2, APH-1 and nicastrin, is a membrane-embedded protease that controls a number of important cellular functions through substrate cleavage. Aberrant cleavage of the amyloid precursor protein (APP) results in aggregation of amyloid-β, which accumulates in the brain and consequently causes Alzheimer's disease. Here we report the three-dimensional structure of an intact human γ-secretase complex at 4.5 Å resolution, determined by cryo-electron-microscopy single-particle analysis. The γ-secretase complex comprises a horseshoe-shaped transmembrane domain, which contains 19 transmembrane segments (TMs), and a large extracellular domain (ECD) from nicastrin, which sits immediately above the hollow space formed by the TM horseshoe. Intriguingly, nicastrin ECD is structurally similar to a large family of peptidases exemplified by the glutamate carboxypeptidase PSMA. This structure serves as an important basis for understanding the functional mechanisms of the γ-secretase complex. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_2677.map.gz | 9.8 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-2677-v30.xml emd-2677.xml | 9.9 KB 9.9 KB | 表示 表示 | EMDBヘッダ |
画像 | EMD-2677.png | 200.1 KB | ||
その他 | emd_2677_additional_1.map.gz emd_2677_half_map_1.map.gz emd_2677_half_map_2.map.gz | 9.8 MB 7.9 MB 7.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2677 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2677 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2677_validation.pdf.gz | 311.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_2677_full_validation.pdf.gz | 310.7 KB | 表示 | |
XML形式データ | emd_2677_validation.xml.gz | 5.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2677 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2677 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_2677.map.gz / 形式: CCP4 / 大きさ: 10.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Reconstruction of human gamma-secretase. The particles were selected by one-step of 3D classification. This map has good density for Nicastrin extracellular domain, but slightly worse density for transmembrane domain. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-添付マップデータ: emd 2677 additional 1.map
ファイル | emd_2677_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-添付マップデータ: emd 2677 half map 1.map
ファイル | emd_2677_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-添付マップデータ: emd 2677 half map 2.map
ファイル | emd_2677_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
-全体 : human gamma-secretase
全体 | 名称: human gamma-secretase |
---|---|
要素 |
|
-超分子 #1000: human gamma-secretase
超分子 | 名称: human gamma-secretase / タイプ: sample / ID: 1000 / 集合状態: tetramer / Number unique components: 1 |
---|---|
分子量 | 実験値: 170 KDa / 理論値: 170 KDa |
-分子 #1: human gamma-secretase
分子 | 名称: human gamma-secretase / タイプ: protein_or_peptide / ID: 1 / コピー数: 4 / 集合状態: tetramer / 組換発現: Yes |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human / 細胞: HEK 293F |
分子量 | 実験値: 170 KDa / 理論値: 170 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: HEK 293F / 組換プラスミド: pMLink |
-実験情報
-構造解析
手法 | ネガティブ染色法, クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 6 mg/mL |
---|---|
緩衝液 | pH: 7.4 / 詳細: 25 mM HEPES, pH 7.4, 150 mM NaCl and amphipol A8-35 |
染色 | タイプ: NEGATIVE / 詳細: cryo-EM |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 90 K / 装置: FEI VITROBOT MARK IV / 手法: Blot for 4S before plunging |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
温度 | 最低: 80 K / 最高: 90 K / 平均: 85 K |
日付 | 2014年2月26日 |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: GATAN K2 (4k x 4k) / デジタル化 - サンプリング間隔: 5 µm / 実像数: 1471 / 平均電子線量: 38 e/Å2 / 詳細: 15 frames were recorded during the imaging. |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 28409 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 4.4 µm / 最小 デフォーカス(公称値): 1.4 µm / 倍率(公称値): 64000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: Each particle |
---|---|
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.5 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: CTFFIND3, RELION 詳細: Use a newly developed statistical movie processing approach to compensate for beam-induced movement. 使用した粒子像数: 144545 |