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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7sxo | ||||||
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タイトル | Yeast Lon (PIM1) with endogenous substrate | ||||||
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![]() | HYDROLASE / Protease / AAA+ ATPase | ||||||
機能・相同性 | ![]() regulation of mitochondrial DNA metabolic process / oxidation-dependent protein catabolic process / mitochondrial respiratory chain complex assembly / endopeptidase La / mitochondrial DNA metabolic process / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein complex assembly / mitochondrion organization / protein folding ...regulation of mitochondrial DNA metabolic process / oxidation-dependent protein catabolic process / mitochondrial respiratory chain complex assembly / endopeptidase La / mitochondrial DNA metabolic process / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein complex assembly / mitochondrion organization / protein folding / single-stranded DNA binding / cellular response to oxidative stress / response to heat / sequence-specific DNA binding / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / mitochondrion / ATP binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() ![]() | ||||||
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: 3.3 Å | ||||||
![]() | Yang, J. / Song, A.S. / Wiseman, R.L. / Lander, G.C. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements. 著者: Jie Yang / Albert S Song / R Luke Wiseman / Gabriel C Lander / ![]() 要旨: Lon protease is a conserved ATP-dependent serine protease composed of an AAA+ domain that mechanically unfolds substrates and a serine protease domain that degrades these unfolded substrates. In ...Lon protease is a conserved ATP-dependent serine protease composed of an AAA+ domain that mechanically unfolds substrates and a serine protease domain that degrades these unfolded substrates. In yeast, dysregulation of Lon protease (PIM1) attenuates lifespan and leads to gross mitochondrial morphological perturbations. Although structures of the bacterial and human Lon protease reveal a hexameric assembly, yeast PIM1 was speculated to form a heptameric assembly and is uniquely characterized by a ∼50-residue insertion between the ATPase and protease domains. To further understand the yeast-specific properties of PIM1, we determined a high-resolution cryo-electron microscopy structure of PIM1 in a substrate-translocating state. Here, we reveal that PIM1 forms a hexamer, conserved with that of bacterial and human Lon proteases, wherein the ATPase domains form a canonical closed spiral that enables pore loop residues to translocate substrates to the protease chamber. In the substrate-translocating state, PIM1 protease domains form a planar protease chamber in an active conformation and are uniquely characterized by a ∼15-residue C-terminal extension. These additional C-terminal residues form an α-helix located along the base of the protease domain. Finally, we did not observe density for the yeast-specific insertion between the ATPase and protease domains, likely due to high conformational flexibility. Biochemical studies to investigate the insertion using constructs that truncated or replaced the insertion with a glycine-serine linker suggest that the yeast-specific insertion is dispensable for PIM1's enzymatic function. Altogether, our structural and biochemical studies highlight unique components of PIM1 machinery and demonstrate evolutionary conservation of Lon protease function. | ||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 589.6 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 1.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.3 MB | 表示 | |
XML形式データ | ![]() | 85.9 KB | 表示 | |
CIF形式データ | ![]() | 127.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 108839.602 Da / 分子数: 6 / 断片: UNP residues 182-1133 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 株: ATCC 204508 / S288c / 遺伝子: PIM1, LON, YBL022C, YBL0440 / 発現宿主: ![]() ![]() #2: タンパク質・ペプチド | | 分子量: 1039.273 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #3: 化合物 | ChemComp-ATP / #4: 化合物 | ChemComp-MG / #5: 化合物 | 研究の焦点であるリガンドがあるか | Y | |
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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 |
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試料調製
構成要素 | 名称: Cryo-EM structure of yeast Lon (PIM1) in complex with endogenous substrate タイプ: COMPLEX / Entity ID: #1-#2 / 由来: MULTIPLE SOURCES |
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由来(天然) | 生物種: ![]() ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
緩衝液 | pH: 8 |
試料 | 濃度: 3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Talos Arctica / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TALOS ARCTICA |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 50 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) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19.2_4158: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 81945 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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