+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5fn2 | ||||||
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タイトル | Cryo-EM structure of gamma secretase in complex with a drug DAPT | ||||||
要素 |
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キーワード | HYDROLASE | ||||||
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 | 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: 4.2 Å | ||||||
データ登録者 | Bai, X.C. / Rajendra, E. / Yang, G.H. / Shi, Y.G. / Scheres, S.H.W. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5fn2.cif.gz | 261.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5fn2.ent.gz | 212.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5fn2.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
文書・要旨 | 5fn2_validation.pdf.gz | 843.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5fn2_full_validation.pdf.gz | 883 KB | 表示 | |
XML形式データ | 5fn2_validation.xml.gz | 41.5 KB | 表示 | |
CIF形式データ | 5fn2_validation.cif.gz | 63 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fn/5fn2 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/5fn2 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 78483.570 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: A DRUG DAPT WAS BOUND TO GAMMA SECRETASE COMPLEX / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: HEK293F / 遺伝子: NCSTN, KIAA0253, UNQ1874/PRO4317 / プラスミド: PMLINK / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q92542 |
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#2: タンパク質 | 分子量: 52651.465 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: A DRUG DAPT WAS BOUND TO GAMMA SECRETASE COMPLEX / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: HEK293F / 遺伝子: PSEN1, AD3, PS1, PSNL1 / プラスミド: PMLINK / 発現宿主: HOMO SAPIENS (ヒト) 参照: UniProt: P49768, 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 |
#3: タンパク質 | 分子量: 29017.943 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: A DRUG DAPT WAS BOUND TO GAMMA SECRETASE COMPLEX / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: HEK293F / 遺伝子: APH1A, PSF, CGI-78, UNQ579/PRO1141 / プラスミド: PMLINK / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q96BI3 |
#4: タンパク質 | 分子量: 12038.029 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: A DRUG DAPT WAS BOUND TO GAMMA SECRETASE COMPLEX / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: HEK293F / 遺伝子: PSENEN, PEN2, MDS033 / プラスミド: PMLINK / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q9NZ42 |
-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 |
-試料調製
構成要素 | 名称: GAMMA SECRETASE / タイプ: COMPLEX |
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緩衝液 | 名称: 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35 / pH: 7.4 / 詳細: 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35 |
試料 | 濃度: 6 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 詳細: LIQUID ETHANE |
-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 / 日付: 2014年12月31日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 81000 X / 倍率(補正後): 35714 X / 最大 デフォーカス(公称値): 2700 nm / 最小 デフォーカス(公称値): 800 nm / Cs: 2 mm |
試料ホルダ | 温度: 85 K |
撮影 | 電子線照射量: 38 e/Å2 フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) |
画像スキャン | デジタル画像の数: 2000 |
-解析
対称性 | 点対称性: C1 (非対称) | ||||||||||||
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3次元再構成 | 解像度: 4.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 51366 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / 対称性のタイプ: POINT | ||||||||||||
精密化 | 最高解像度: 4.2 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 4.2 Å
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