+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5a63 | ||||||||||||
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タイトル | Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolution. | ||||||||||||
要素 |
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キーワード | HYDROLASE (加水分解酵素) / CRYO-EM (低温電子顕微鏡法) / HUMAN GAMMA-SECRETASE (Γ-セクレターゼ) / MEMBRANE PROTEIN (膜タンパク質) | ||||||||||||
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 / protein catabolic process at postsynapse / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / 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 / protein catabolic process at postsynapse / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / positive regulation of amyloid precursor protein biosynthetic process / Noncanonical activation of NOTCH3 / positive regulation of endopeptidase activity / choline transport / Notch receptor processing / central nervous system myelination / sequestering of calcium ion / membrane protein intracellular domain proteolysis / synaptic vesicle targeting / negative regulation of axonogenesis / regulation of resting membrane potential / T cell activation involved in immune response / skin morphogenesis / NOTCH4 Activation and Transmission of Signal to the Nucleus / growth factor receptor binding / neural retina development / dorsal/ventral neural tube patterning / regulation of synaptic vesicle cycle / L-glutamate import across plasma membrane / myeloid dendritic cell differentiation / Regulated proteolysis of p75NTR / amyloid precursor protein metabolic process / regulation of phosphorylation / metanephros development / locomotion / brain morphogenesis / glutamate receptor signaling pathway / endoplasmic reticulum calcium ion homeostasis / nuclear outer membrane / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of canonical Wnt signaling pathway / aggresome / regulation of long-term synaptic potentiation / embryonic limb morphogenesis / skeletal system morphogenesis / positive regulation of amyloid fibril formation / cell fate specification / regulation of postsynapse organization / positive regulation of dendritic spine development / 繊毛 / myeloid cell homeostasis / azurophil granule membrane / dopamine receptor signaling pathway / 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 / Golgi cisterna membrane / adult behavior / positive regulation of receptor recycling / mitochondrial transport / positive regulation of catalytic activity / regulation of neuron projection development / heart looping / blood vessel development / amyloid precursor protein catabolic process / cerebral cortex cell migration / 小胞体 / protein glycosylation / amyloid-beta formation / negative regulation of apoptotic signaling pathway / autophagosome assembly / membrane protein ectodomain proteolysis / endopeptidase activator activity / EPH-ephrin mediated repulsion of cells / neuron development / 小胞体 / Nuclear signaling by ERBB4 / hematopoietic progenitor cell differentiation / somitogenesis / amyloid-beta metabolic process / T cell proliferation / negative regulation of ubiquitin-dependent protein catabolic process / Notchシグナリング / regulation of synaptic transmission, glutamatergic / NOTCH2 Activation and Transmission of Signal to the Nucleus / cellular response to calcium ion / neuron projection maintenance / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Degradation of the extracellular matrix / cerebellum development / positive regulation of glycolytic process / post-embryonic development / dendritic shaft / thymus development / negative regulation of protein phosphorylation / epithelial cell proliferation / PDZ domain binding / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / 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: 3.4 Å | ||||||||||||
データ登録者 | Bai, X. / Yan, C. / Yang, G. / Lu, P. / Ma, D. / Sun, L. / Zhou, R. / Scheres, S.H.W. / Shi, Y. | ||||||||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: An atomic structure of human γ-secretase. 著者: Xiao-Chen Bai / Chuangye Yan / Guanghui Yang / Peilong Lu / Dan Ma / Linfeng Sun / Rui Zhou / Sjors H W Scheres / Yigong Shi / 要旨: Dysfunction of the intramembrane protease γ-secretase is thought to cause Alzheimer's disease, with most mutations derived from Alzheimer's disease mapping to the catalytic subunit presenilin 1 (PS1) ...Dysfunction of the intramembrane protease γ-secretase is thought to cause Alzheimer's disease, with most mutations derived from Alzheimer's disease mapping to the catalytic subunit presenilin 1 (PS1). Here we report an atomic structure of human γ-secretase at 3.4 Å resolution, determined by single-particle cryo-electron microscopy. Mutations derived from Alzheimer's disease affect residues at two hotspots in PS1, each located at the centre of a distinct four transmembrane segment (TM) bundle. TM2 and, to a lesser extent, TM6 exhibit considerable flexibility, yielding a plastic active site and adaptable surrounding elements. The active site of PS1 is accessible from the convex side of the TM horseshoe, suggesting considerable conformational changes in nicastrin extracellular domain after substrate recruitment. Component protein APH-1 serves as a scaffold, anchoring the lone transmembrane helix from nicastrin and supporting the flexible conformation of PS1. Ordered phospholipids stabilize the complex inside the membrane. Our structure serves as a molecular basis for mechanistic understanding of γ-secretase function. | ||||||||||||
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 | 5a63.cif.gz | 263 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5a63.ent.gz | 211.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5a63.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/a6/5a63 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/5a63 | HTTPS FTP |
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-関連構造データ
関連構造データ | 2677M 2678M 3061MC 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 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10194 (タイトル: An atomic structure of human gamma-secretase / Data size: 11.7 TB Data #1: Unaligned multi-frame micrographs of human gamma-secretase [micrographs - multiframe]) |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 2種, 2分子 AB
#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 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: HEK 293F / 遺伝子: NCSTN, KIAA0253, UNQ1874/PRO4317 / 細胞株 (発現宿主): HEK 293F / 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: 52713.535 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: HEK 293F / 遺伝子: PSEN1, AD3, PS1, PSNL1 / 細胞株 (発現宿主): HEK 293F / 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 |
-Gamma-secretase subunit ... , 2種, 2分子 CD
#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 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: HEK 293F / 遺伝子: APH1A, PSF, CGI-78, UNQ579/PRO1141 / 細胞株 (発現宿主): HEK 293F / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q96BI3 |
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#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 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: HEK 293F / 遺伝子: PSENEN, PEN2, MDS033 / 細胞株 (発現宿主): HEK 293F / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q9NZ42 |
-糖 , 3種, 11分子
#5: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #6: 多糖 | beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #7: 糖 | ChemComp-NAG / |
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-非ポリマー , 1種, 2分子
#8: 化合物 |
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-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: HUMAN GAMMA-SECRETASEΓ-セクレターゼ / 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: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 85, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 4 SECONDS BEFORE PLUNGING, |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F30 / 日付: 2014年10月2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 FIELDBright-field microscopy / 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): 3200 nm / 最小 デフォーカス(公称値): 700 nm / Cs: 2.7 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 (4k x 4k) |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: EACH PARTICLE | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 解像度: 3.4 Å / 粒子像の数: 159549 倍率補正: CROSS- -CORRELATION DENSITIES WITHIN SPHERICAL SHELL 詳細: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3061. (DEPOSITION ID: 13527). 対称性のタイプ: POINT | ||||||||||||
精密化 | 最高解像度: 3.4 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 3.4 Å
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