+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4uis | ||||||
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タイトル | The cryoEM structure of human gamma-Secretase complex | ||||||
要素 |
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キーワード | HYDROLASE / GAMMA-SECRETASE | ||||||
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 / 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 / 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 / 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 / viral release from host cell by cytolysis / 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 / peptidoglycan catabolic 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 / neuron migration 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: 4.4 Å | ||||||
データ登録者 | Sun, L. / Zhao, L. / Yang, G. / Yan, C. / Zhou, R. / Zhou, X. / Xie, T. / Zhao, Y. / Wu, S. / Li, X. / Shi, Y. | ||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2015 タイトル: Structural basis of human γ-secretase assembly. 著者: Linfeng Sun / Lingyun Zhao / Guanghui Yang / Chuangye Yan / Rui Zhou / Xiaoyuan Zhou / Tian Xie / Yanyu Zhao / Shenjie Wu / Xueming Li / Yigong Shi / 要旨: The four-component intramembrane protease γ-secretase is intricately linked to the development of Alzheimer's disease. Despite recent structural advances, the transmembrane segments (TMs) of γ- ...The four-component intramembrane protease γ-secretase is intricately linked to the development of Alzheimer's disease. Despite recent structural advances, the transmembrane segments (TMs) of γ-secretase remain to be specifically assigned. Here we report a 3D structure of human γ-secretase at 4.32-Å resolution, determined by single-particle, electron cryomicroscopy in the presence of digitonin and with a T4 lysozyme fused to the amino terminus of presenilin 1 (PS1). The overall structure of this human γ-secretase is very similar to that of wild-type γ-secretase determined in the presence of amphipols. The 20 TMs are unambiguously assigned to the four components, revealing principles of subunit assembly. Within the transmembrane region, PS1 is centrally located, with its amino-terminal fragment (NTF) packing against Pen-2 and its carboxyl-terminal fragment (CTF) interacting with Aph-1. The only TM of nicastrin associates with Aph-1 at the thick end of the TM horseshoe, and the extracellular domain of nicastrin directly binds Pen-2 at the thin end. TM6 and TM7 in PS1, which harbor the catalytic aspartate residues, are located on the convex side of the TM horseshoe. This structure serves as an important framework for understanding the function and mechanism of γ-secretase. | ||||||
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 | 4uis.cif.gz | 281.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4uis.ent.gz | 235.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4uis.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 | 4uis_validation.pdf.gz | 817.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4uis_full_validation.pdf.gz | 851.7 KB | 表示 | |
XML形式データ | 4uis_validation.xml.gz | 35.7 KB | 表示 | |
CIF形式データ | 4uis_validation.cif.gz | 55.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ui/4uis ftp://data.pdbj.org/pub/pdb/validation_reports/ui/4uis | 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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1 |
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-要素
#1: タンパク質 | 分子量: 63331.977 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 (発現宿主): HEK 293S / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: Q92542*PLUS |
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#2: タンパク質 | 分子量: 23547.639 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 (発現宿主): HEK 293S / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: P49768*PLUS |
#3: タンパク質 | 分子量: 16698.539 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 (発現宿主): HEK 293S / 発現宿主: HOMO SAPIENS (ヒト) |
#4: タンパク質 | 分子量: 5294.518 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 (発現宿主): HEK 293S / 発現宿主: HOMO SAPIENS (ヒト) |
#5: タンパク質 | 分子量: 18435.207 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 (発現宿主): HEK 293S / 発現宿主: HOMO SAPIENS (ヒト) / 参照: UniProt: A0A097J809, UniProt: D9IEF7*PLUS, lysozyme |
-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: T4-LYSOZYME FUSION GAMMA- SECRETASE / タイプ: COMPLEX |
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緩衝液 | 名称: 0.1% DIGITONIN, 25 MM HEPES, PH 7.4, AND 150 MM NACL. pH: 7.4 詳細: 0.1% DIGITONIN, 25 MM HEPES, PH 7.4, AND 150 MM NACL. |
試料 | 濃度: 4.2 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- 277, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING, |
-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22日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 1.4 mm |
撮影 | 電子線照射量: 4.5 e/Å2 フィルム・検出器のモデル: DIRECT ELECTRON DE-12 (4k x 3k) |
画像スキャン | デジタル画像の数: 2000 |
-解析
EMソフトウェア |
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対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 解像度: 4.4 Å / 粒子像の数: 177207 / ピクセルサイズ(公称値): 1.32 Å / ピクセルサイズ(実測値): 1.32 Å 詳細: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2974. (DEPOSITION ID: 13293 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL / 詳細: METHOD--FLEXIBLE | ||||||||||||
原子モデル構築 | PDB-ID: 4R12 | ||||||||||||
精密化 | 最高解像度: 4.4 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 4.4 Å
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