+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-21250 | ||||||||||||
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タイトル | Cryo-EM structure of the C-terminal half of the Parkinson's Disease-linked protein Leucine Rich Repeat Kinase 2 (LRRK2) | ||||||||||||
マップデータ | 3.8A signal subtracted locally filtered cryo-EM map of C-terminal half of Leucine Rich Repeat Kinase 2 (LRRK2) | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 peroxidase inhibitor activity / caveola neck / negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation / negative regulation of protein processing involved in protein targeting to mitochondrion / Wnt signalosome assembly / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / regulation of neuron maturation / tangential migration from the subventricular zone to the olfactory bulb ...peroxidase inhibitor activity / caveola neck / negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation / negative regulation of protein processing involved in protein targeting to mitochondrion / Wnt signalosome assembly / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / regulation of neuron maturation / tangential migration from the subventricular zone to the olfactory bulb / protein localization to endoplasmic reticulum exit site / GTP-dependent protein kinase activity / regulation of neuroblast proliferation / regulation of ER to Golgi vesicle-mediated transport / regulation of synaptic vesicle transport / negative regulation of late endosome to lysosome transport / regulation of mitochondrial depolarization / negative regulation of protein targeting to mitochondrion / positive regulation of dopamine receptor signaling pathway / regulation of lysosomal lumen pH / regulation of CAMKK-AMPK signaling cascade / amphisome / mitochondrion localization / cytoplasmic side of mitochondrial outer membrane / co-receptor binding / regulation of retrograde transport, endosome to Golgi / negative regulation of excitatory postsynaptic potential / negative regulation of autophagosome assembly / regulation of dopamine receptor signaling pathway / positive regulation of microglial cell activation / neuron projection arborization / positive regulation of synaptic vesicle endocytosis / JUN kinase kinase kinase activity / olfactory bulb development / regulation of dendritic spine morphogenesis / regulation of protein kinase A signaling / multivesicular body, internal vesicle / striatum development / protein localization to mitochondrion / cellular response to dopamine / presynaptic cytosol / positive regulation of protein autoubiquitination / endoplasmic reticulum organization / positive regulation of programmed cell death / Wnt signalosome / GTP metabolic process / regulation of canonical Wnt signaling pathway / negative regulation of protein processing / syntaxin-1 binding / regulation of reactive oxygen species metabolic process / negative regulation of GTPase activity / regulation of locomotion / オートファゴソーム / protein kinase A binding / exploration behavior / regulation of synaptic vesicle exocytosis / Golgi-associated vesicle / PTK6 promotes HIF1A stabilization / clathrin binding / negative regulation of macroautophagy / lysosome organization / regulation of mitochondrial fission / neuromuscular junction development / intracellular distribution of mitochondria / Golgi organization / positive regulation of nitric-oxide synthase biosynthetic process / locomotory exploration behavior / 微絨毛 / Rho protein signal transduction / cellular response to organic cyclic compound / MAP kinase kinase kinase activity / canonical Wnt signaling pathway / positive regulation of protein kinase activity / cellular response to manganese ion / endoplasmic reticulum exit site / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of autophagy / JNK cascade / regulation of synaptic transmission, glutamatergic / excitatory postsynaptic potential / regulation of membrane potential / cellular response to starvation / dendrite cytoplasm / GTPase activator activity / mitochondrion organization / tubulin binding / SNARE binding / neuron projection morphogenesis / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of protein ubiquitination / regulation of autophagy / determination of adult lifespan / calcium-mediated signaling / ミトコンドリア / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / peptidyl-threonine phosphorylation / regulation of protein stability / positive regulation of MAP kinase activity / ゴルジ体 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: 3.5 Å | ||||||||||||
データ登録者 | Leschziner A / Deniston C / Lahiri I | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Nature / 年: 2020 タイトル: Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. 著者: C K Deniston / J Salogiannis / S Mathea / D M Snead / I Lahiri / M Matyszewski / O Donosa / R Watanabe / J Böhning / A K Shiau / S Knapp / E Villa / S L Reck-Peterson / A E Leschziner / 要旨: Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease and is also linked to its idiopathic form. LRRK2 has been proposed to function in membrane ...Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease and is also linked to its idiopathic form. LRRK2 has been proposed to function in membrane trafficking and colocalizes with microtubules. Despite the fundamental importance of LRRK2 for understanding and treating Parkinson's disease, structural information on the enzyme is limited. Here we report the structure of the catalytic half of LRRK2, and an atomic model of microtubule-associated LRRK2 built using a reported cryo-electron tomography in situ structure. We propose that the conformation of the LRRK2 kinase domain regulates its interactions with microtubules, with a closed conformation favouring oligomerization on microtubules. We show that the catalytic half of LRRK2 is sufficient for filament formation and blocks the motility of the microtubule-based motors kinesin 1 and cytoplasmic dynein 1 in vitro. Kinase inhibitors that stabilize an open conformation relieve this interference and reduce the formation of LRRK2 filaments in cells, whereas inhibitors that stabilize a closed conformation do not. Our findings suggest that LRRK2 can act as a roadblock for microtubule-based motors and have implications for the design of therapeutic LRRK2 kinase inhibitors. | ||||||||||||
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_21250.map.gz | 100.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-21250-v30.xml emd-21250.xml | 28.3 KB 28.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_21250_fsc_1.xml emd_21250_fsc_2.xml | 12.7 KB 12.7 KB | 表示 表示 | FSCデータファイル |
画像 | emd_21250.png | 154 KB | ||
その他 | emd_21250_additional_1.map.gz emd_21250_additional_2.map.gz emd_21250_additional_3.map.gz emd_21250_half_map_1.map.gz emd_21250_half_map_2.map.gz | 162.5 MB 159.6 MB 159.6 MB 136.1 MB 136 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-21250 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21250 | 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_21250.map.gz / 形式: CCP4 / 大きさ: 172.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | 3.8A signal subtracted locally filtered cryo-EM map of C-terminal half of Leucine Rich Repeat Kinase 2 (LRRK2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: 3.47A C3 symmetric locally filtered cryo-EM map of...
ファイル | emd_21250_additional_1.map | ||||||||||||
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注釈 | 3.47A C3 symmetric locally filtered cryo-EM map of C-terminal half of Leucine Rich Repeat Kinase 2 (LRRK2). | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Half map 1 of C3 symmetric map
ファイル | emd_21250_additional_2.map | ||||||||||||
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注釈 | Half map 1 of C3 symmetric map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Half map 2 of C3 symmetric map
ファイル | emd_21250_additional_3.map | ||||||||||||
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注釈 | Half map 2 of C3 symmetric map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 1 of signal subtracted map
ファイル | emd_21250_half_map_1.map | ||||||||||||
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注釈 | Half map 1 of signal subtracted map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 2 of signal subtracted map
ファイル | emd_21250_half_map_2.map | ||||||||||||
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注釈 | Half map 2 of signal subtracted map | ||||||||||||
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 : The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) p...
全体 | 名称: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) protein. |
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要素 |
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-超分子 #1: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) p...
超分子 | 名称: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) protein. タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 / 詳細: C-terminal half runs from residue 1327-2527. |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
分子量 | 理論値: 137 KDa |
-分子 #1: Leucine-rich repeat serine/threonine-protein kinase 2
分子 | 名称: Leucine-rich repeat serine/threonine-protein kinase 2 タイプ: protein_or_peptide / ID: 1 / 詳細: C-terminal residues 1330-2527 / コピー数: 1 / 光学異性体: LEVO / EC番号: non-specific serine/threonine protein kinase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 136.943609 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: KKAVPYNRMK LMIVGN(TPO)GSG KTTLLQQLMK TKKSDLGMQS ATVGIDVKDW PIQIRDKRKR DLVLNVWDFA GREEFY STH PHFMTQRALY LAVYDLSKGQ AEVDAMKPWL FNIKARASSS PVILVGTHLD VSDEKQRKAC MSKITKELLN KRGFPAI RD ...文字列: KKAVPYNRMK LMIVGN(TPO)GSG KTTLLQQLMK TKKSDLGMQS ATVGIDVKDW PIQIRDKRKR DLVLNVWDFA GREEFY STH PHFMTQRALY LAVYDLSKGQ AEVDAMKPWL FNIKARASSS PVILVGTHLD VSDEKQRKAC MSKITKELLN KRGFPAI RD YHFVNATEES DALAKLRKTI INESLNFKIR DQLVVGQLIP DCYVELEKII LSERKNVPIE FPVIDRKRLL QLVRENQL Q LDENELPHAV HFLNESGVLL HFQDPALQLS DLYFVEPKWL CKIMAQILTV KVEGCPKHPK GIISRRDVEK FLSKKRKFP KNYMSQYFKL LEKFQIALPI GEEYLLVPSS LSDHRPVIEL PHCENSEIII RLYEMPYFPM GFWSRLINRL LEISPYMLSG RERALRPNR MYWRQGIYLN WSPEAYCLVG SEVLDNHPES FLKITVPSCR KGCILLGQVV DHIDSLMEEW FPGLLEIDIC G EGETLLKK WALYSFNDGE EHQKILLDDL MKKAEEGDLL VNPDQPRLTI PISQIAPDLI LADLPRNIML NNDELEFEQA PE FLLGDGS FGSVYRAAYE GEEVAVKIFN KHTSLRLLRQ ELVVLCHLHH PSLISLLAAG IRPRMLVMEL ASKGSLDRLL QQD KASLTR TLQHRIALHV ADGLRYLHSA MIIYRDLKPH NVLLFTLYPN AAIIAKIADY GIAQYCCRMG IKTSEGTPGF RAPE VARGN VIYNQQADVY SFGLLLYDIL TTGGRIVEGL KFPNEFDELE IQGKLPDPVK EYGCAPWPMV EKLIKQCLKE NPQER PTSA QVFDILNSAE LVCLTRRILL PKNVIVECMV ATHHNSRNAS IWLGCGHTDR GQLSFLDLNT EGYTSEEVAD SRILCL ALV HLPVEKESWI VSGTQSGTLL VINTEDGKKR HTLEKMTDSV TCLYCNSFSK QSKQKNFLLV GTADGKLAIF EDKTVKL KG AAPLKILNIG NVSTPLMCLS ESTNSTERNV MWGGCGTKIF SFSNDFTIQK LIETRTSQLF SYAAFSDSNI ITVVVDTA L YIAKQNSPVV EVWDKKTEKL CGLIDCVHFL REVMVKENKE SKHKMSYSGR VKTLCLQKNT ALWIGTGGGH ILLLDLSTR RLIRVIYNFC NSVRVMMTAQ LGSLKNVMLV LGYNRKNTEG TQKQKEIQSC LTVWDINLPH EVQNLEKHIE VRKELAEKMR RTSVE |
-分子 #2: GUANOSINE-5'-DIPHOSPHATE
分子 | 名称: GUANOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 2 / コピー数: 1 / 式: GDP |
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分子量 | 理論値: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-分子 #3: MAGNESIUM ION
分子 | 名称: MAGNESIUM ION / タイプ: ligand / ID: 3 / コピー数: 1 / 式: MG |
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分子量 | 理論値: 24.305 Da |
-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 | 0.5 mg/mL | |||||||||||||||||||||
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緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: Quantifoil, UltrAuFoil, R1.2/1.3 / 材質: GOLD / 前処理 - タイプ: GLOW DISCHARGE | |||||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK II | |||||||||||||||||||||
詳細 | 4uM concentration |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.8 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 130000 |
特殊光学系 | エネルギーフィルター - 名称: GIF 2002 |
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 |
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 / 撮影したグリッド数: 1 / 実像数: 3826 / 平均露光時間: 8.0 sec. / 平均電子線量: 6.65 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |