+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3238 | |||||||||
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タイトル | Cryo-EM structure of gamma secretase in class 1 of the apo-state ensemble | |||||||||
マップデータ | Reconstruction of gamma secretase in class 1 of the apo-state ensemble | |||||||||
試料 |
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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: 4.1 Å | |||||||||
データ登録者 | Bai XC / Rajendra E / Yang GH / Shi YG / Scheres SHW | |||||||||
引用 | ジャーナル: Elife / 年: 2015 タイトル: Sampling the conformational space of the catalytic subunit of human γ-secretase. 著者: Xiao-chen Bai / Eeson Rajendra / Guanghui Yang / Yigong Shi / Sjors H W Scheres / 要旨: Human γ-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein ...Human γ-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein lead to Alzheimer's disease. Our previous cryo-EM structure of γ-secretase revealed considerable disorder in its catalytic subunit presenilin. Here, we describe an image classification procedure that characterizes molecular plasticity at the secondary structure level, and apply this method to identify three distinct conformations in our previous sample. In one of these conformations, an additional transmembrane helix is visible that cannot be attributed to the known components of γ-secretase. In addition, we present a γ-secretase structure in complex with the dipeptidic inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT). Our results reveal how conformational mobility in the second and sixth transmembrane helices of presenilin is greatly reduced upon binding of DAPT or the additional helix, and form the basis for a new model of how substrate enters the transmembrane domain. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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_3238.map.gz | 20.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3238-v30.xml emd-3238.xml | 10.1 KB 10.1 KB | 表示 表示 | EMDBヘッダ |
画像 | EMD-3238.jpg | 226 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3238 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3238 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3238_validation.pdf.gz | 273.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3238_full_validation.pdf.gz | 272.5 KB | 表示 | |
XML形式データ | emd_3238_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-3238 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3238 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「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_3238.map.gz / 形式: CCP4 / 大きさ: 21.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of gamma secretase in class 1 of the apo-state ensemble | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : human gamma secretase in class 1 of the apo-state ensemble
全体 | 名称: human gamma secretase in class 1 of the apo-state ensemble |
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要素 |
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-超分子 #1000: human gamma secretase in class 1 of the apo-state ensemble
超分子 | 名称: human gamma secretase in class 1 of the apo-state ensemble タイプ: sample / ID: 1000 / 集合状態: Heterotetramer / Number unique components: 1 |
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分子量 | 実験値: 170 KDa / 理論値: 170 KDa |
-分子 #1: gamma-secretase
分子 | 名称: gamma-secretase / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 集合状態: Heterotetramer / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human / 細胞: HEK293F / 細胞中の位置: membrane |
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 |
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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 |
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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 |
グリッド | 詳細: 300 mesh Au 1.2/1.3 Quantifoil grid, glow discharged for 1 minute |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 85 K / 装置: FEI VITROBOT MARK IV / 手法: Blot for 4 seconds before plunging |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 80 K / 最高: 90 K / 平均: 85 K |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 81000 magnification |
特殊光学系 | エネルギーフィルター - 名称: Gatan Quantum エネルギーフィルター - エネルギー下限: 0.0 eV エネルギーフィルター - エネルギー上限: 20.0 eV |
日付 | 2014年10月25日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) デジタル化 - サンプリング間隔: 5 µm / 実像数: 2925 / 平均電子線量: 38 e/Å2 詳細: Use a newly developed statistical movie processing and particle polishing approach to compensate for beam-induced movement and reduce the effect of radiation-damage |
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): 35714 / 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): 3.2 µm / 最小 デフォーカス(公称値): 0.7 µm / 倍率(公称値): 81000 |
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 |
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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: 4.1 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: CTFFIND4, RELION / 使用した粒子像数: 63873 |