+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-7041 | |||||||||||||||
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タイトル | Cryo-EM structure of human insulin degrading enzyme in complex with insulin | |||||||||||||||
マップデータ | This is the sharpened map from the final, Insulin degrading enzyme in complex with insulin | |||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of aerobic respiration / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / peptide catabolic process / IRS activation / Insulin processing / regulation of protein secretion / amyloid-beta clearance / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / peroxisomal matrix / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / amyloid-beta metabolic process / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / peptide binding / proteolysis involved in protein catabolic process / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / Peroxisomal protein import / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / protein catabolic process / regulation of synaptic plasticity / vasodilation / hormone activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / positive regulation of protein catabolic process / glucose metabolic process / regulation of protein localization / glucose homeostasis / virus receptor activity / positive regulation of protein binding / insulin receptor signaling pathway / cell-cell signaling / peroxisome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / basolateral plasma membrane / endopeptidase activity / protease binding 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 / 解像度: 3.7 Å | |||||||||||||||
データ登録者 | Zhang Z / Liang WG / Bailey LJ / Tan YZ / Wei H / Kossiakoff AA / Carragher B / Potter SC / Tang WJ | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Elife / 年: 2018 タイトル: Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. 著者: Zhening Zhang / Wenguang G Liang / Lucas J Bailey / Yong Zi Tan / Hui Wei / Andrew Wang / Mara Farcasanu / Virgil A Woods / Lauren A McCord / David Lee / Weifeng Shang / Rebecca Deprez- ...著者: Zhening Zhang / Wenguang G Liang / Lucas J Bailey / Yong Zi Tan / Hui Wei / Andrew Wang / Mara Farcasanu / Virgil A Woods / Lauren A McCord / David Lee / Weifeng Shang / Rebecca Deprez-Poulain / Benoit Deprez / David R Liu / Akiko Koide / Shohei Koide / Anthony A Kossiakoff / Sheng Li / Bridget Carragher / Clinton S Potter / Wei-Jen Tang / 要旨: Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes ...Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes peptides that tend to form amyloid fibrils remained unsolved. We used cryoEM to understand both the apo- and insulin-bound dimeric IDE states, revealing that IDE displays a large opening between the homologous ~55 kDa N- and C-terminal halves to allow selective substrate capture based on size and charge complementarity. We also used cryoEM, X-ray crystallography, SAXS, and HDX-MS to elucidate the molecular basis of how amyloidogenic peptides stabilize the disordered IDE catalytic cleft, thereby inducing selective degradation by substrate-assisted catalysis. Furthermore, our insulin-bound IDE structures explain how IDE processively degrades insulin by stochastically cutting either chain without breaking disulfide bonds. Together, our studies provide a mechanism for how IDE selectively degrades amyloidogenic peptides and offers structural insights for developing IDE-based therapies. | |||||||||||||||
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_7041.map.gz | 7.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-7041-v30.xml emd-7041.xml | 26.9 KB 26.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_7041_fsc.xml | 11.4 KB | 表示 | FSCデータファイル |
画像 | emd_7041.png | 56.3 KB | ||
マスクデータ | emd_7041_msk_1.map | 125 MB | マスクマップ | |
その他 | emd_7041_additional.map.gz emd_7041_half_map_1.map.gz emd_7041_half_map_2.map.gz | 97.6 MB 98.4 MB 98.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-7041 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7041 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_7041_validation.pdf.gz | 552.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_7041_full_validation.pdf.gz | 552.2 KB | 表示 | |
XML形式データ | emd_7041_validation.xml.gz | 18.6 KB | 表示 | |
CIF形式データ | emd_7041_validation.cif.gz | 24.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7041 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7041 | HTTPS FTP |
-関連構造データ
関連構造データ | 6b3qMC 6bfcMC 7062C 7065C 7066C 7090C 7091C 7092C 7093C 5wobC 6b70C 6b7yC 6b7zC 6bf6C 6bf7C 6bf8C 6bf9C C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ |
-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_7041.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | This is the sharpened map from the final, Insulin degrading enzyme in complex with insulin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.073 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
-マスク #1
ファイル | emd_7041_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: This is the full, unfiltered map from final...
ファイル | emd_7041_additional.map | ||||||||||||
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注釈 | This is the full, unfiltered map from final refinement for insulin degrading enzyme in complex with insulin | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: This is the first half map from the...
ファイル | emd_7041_half_map_1.map | ||||||||||||
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注釈 | This is the first half map from the final refinement for insulin degrading enzyme in complex with insulin | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: This is the second half map from the...
ファイル | emd_7041_half_map_2.map | ||||||||||||
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注釈 | This is the second half map from the final refinement for insulin degrading enzyme in complex with insulin | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Insulin degrading enzyme/Insulin
全体 | 名称: Insulin degrading enzyme/Insulin |
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要素 |
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-超分子 #1: Insulin degrading enzyme/Insulin
超分子 | 名称: Insulin degrading enzyme/Insulin / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: Cryo-EM structure of human insulin degrading enzyme in complex with insulin |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli (大腸菌) / 組換株: BL |
分子量 | 実験値: 100 KDa |
-分子 #1: Insulin-degrading enzyme
分子 | 名称: Insulin-degrading enzyme / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO / EC番号: insulysin |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 114.561562 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MHHHHHHAAG IPMNNPAIKR IGNHITKSPE DKREYRGLEL ANGIKVLLIS DPTTDKSSAA LDVHIGSLSD PPNIAGLSHF LEHMLFLGT KKYPKENEYS QFLSEHAGSS NAFTSGEHTN YYFDVSHEHL EGALDRFAQF FLSPLFDESA KDREVNAVDS E HEKNVMND ...文字列: MHHHHHHAAG IPMNNPAIKR IGNHITKSPE DKREYRGLEL ANGIKVLLIS DPTTDKSSAA LDVHIGSLSD PPNIAGLSHF LEHMLFLGT KKYPKENEYS QFLSEHAGSS NAFTSGEHTN YYFDVSHEHL EGALDRFAQF FLSPLFDESA KDREVNAVDS E HEKNVMND AWRLFQLEKA TGNPKHPFSK FGTGNKYTLE TRPNQEGIDV RQELLKFHSA YYSSNLMAVV VLGRESLDDL TN LVVKLFS EVENKNVPLP EFPEHPFQEE HLKQLYKIVP IKDIRNLYVT FPIPDLQKYY KSNPGHYLGH LIGHEGPGSL LSE LKSKGW VNTLVGGQKE GARGFMFFII NVDLTEEGLL HVEDIILHMF QYIQKLRAEG PQEWVFQELK DLNAVAFRFK DKER PRGYT SKIAGILHYY PLEEVLTAEY LLEEFRPDLI EMVLDKLRPE NVRVAIVSKS FEGKTDRTEE WYGTQYKQEA IPDEV IKKW QNADLNGKFK LPTKNEFIPT NFEILPLEKE ATPYPALIKD TAMSKLWFKQ DDKFFLPKAN LNFEFFSPFA YVDPLH SNM AYLYLELLKD SLNEYAYAAE LAGLSYDLQN TIYGMYLSVK GYNDKQPILL KKIIEKMATF EIDEKRFEII KEAYMRS LN NFRAEQPHQH AMYYLRLLMT EVAWTKDELK EALDDVTLPR LKAFIPQLLS RLHIEALLHG NITKQAALGI MQMVEDTL I EHAHTKPLLP SQLVRYREVQ LPDRGWFVYQ QRNEVHNNSG IEIYYQTDMQ STSENMFLEL FAQIISEPAF NTLRTKEQL GYIVFSGPRR ANGIQGLRFI IQSEKPPHYL ESRVEAFLIT MEKSIEDMTE EAFQKHIQAL AIRRLDKPKK LSAESAKYWG EIISQQYNF DRDNTEVAYL KTLTKEDIIK FYKEMLAVDA PRRHKVSVHV LAREMDSNPV VGEFPAQNDI NLSQAPALPQ P EVIQNMTE FKRGLPLFPL VKPHINFMAA KL |
-分子 #2: Insulin
分子 | 名称: Insulin / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 11.989862 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MALWMRLLPL LALLALWGPD PAAAFVNQHL CGSHLVEALY LVCGERGFFY TPKTRREAED LQVGQVELGG GPGAGSLQPL ALEGSLQKR GIVEQCCTSI CSLYQLENYC N |
-実験情報
-構造解析
手法 | 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 | 0.3 mg/mL | ||||||||||||
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緩衝液 | pH: 7.8 構成要素:
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グリッド | モデル: homemade nanowire grid / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 支持フィルム - Film thickness: 10.0 nm / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: OTHER / 前処理 - 気圧: 0.001 kPa | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 85 % / チャンバー内温度: 298 K / 装置: HOMEMADE PLUNGER 詳細: The cryo grids were made using Spotiton and homemade plunger. | ||||||||||||
詳細 | The sample was monodisperse |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 70.0 K / 最高: 70.0 K |
アライメント法 | Coma free - Residual tilt: 10.0 mrad |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / デジタル化 - サイズ - 横: 3710 pixel / デジタル化 - サイズ - 縦: 3838 pixel / デジタル化 - サンプリング間隔: 5.0 µm / デジタル化 - 画像ごとのフレーム数: 1-50 / 撮影したグリッド数: 3 / 実像数: 3085 / 平均露光時間: 10.0 sec. / 平均電子線量: 71.4 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 倍率(補正後): 46598 / 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): 2.2 µm 最小 デフォーカス(公称値): 0.9400000000000001 µm 倍率(公称値): 22500 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |