+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6vp8 | ||||||||||||
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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) | ||||||||||||
要素 | (Leucine-rich repeat serine/threonine-protein kinase 2) x 3 | ||||||||||||
キーワード | SIGNALING PROTEIN / Kinase (キナーゼ) / GTPase (GTPアーゼ) | ||||||||||||
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 / Wnt signalosome / positive regulation of programmed cell death / 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 | 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: 3.5 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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6vp8.cif.gz | 333.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6vp8.ent.gz | 266.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6vp8.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/vp/6vp8 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/6vp8 | HTTPS FTP |
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-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: 136614.188 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: C-terminal residues 1330-2527 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LRRK2, PARK8 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q5S007, non-specific serine/threonine protein kinase, 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 |
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#2: タンパク質 | 分子量: 32254.275 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: COR domain, residues 1670-1950 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LRRK2, PARK8 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q5S007, non-specific serine/threonine protein kinase, 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 |
#3: タンパク質 | 分子量: 40178.562 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: WD40 domain, residues 2140-2498 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LRRK2 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q5S007, non-specific serine/threonine protein kinase, 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 |
研究の焦点であるリガンドがあるか | Y |
-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: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) protein タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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分子量 | 値: 0.137 MDa / 実験値: NO | |||||||||||||||||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | |||||||||||||||||||||||||||||||||||
由来(組換発現) | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) | |||||||||||||||||||||||||||||||||||
緩衝液 | pH: 7.4 | |||||||||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: 4uM concentration | |||||||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのタイプ: Quantifoil, UltrAuFoil, R1.2/1.3 | |||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K |
-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 |
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): 130000 X / 最大 デフォーカス(公称値): 1800 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 8 sec. / 電子線照射量: 6.65 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 1 / 実像数: 3826 |
電子光学装置 | エネルギーフィルター名称: GIF 2002 |
画像スキャン | 動画フレーム数/画像: 40 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: Per-particle CTF values / タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 836956 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C3 (3回回転対称) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 70953 詳細: For the signal subtracted map, 105,787 particles went into the final map that achieved 3.8A resolution 対称性のタイプ: POINT |