+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8726 | ||||||||||||||||||
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タイトル | Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3) | ||||||||||||||||||
マップデータ | V-ATPase:SidK complex, rotational state 3 | ||||||||||||||||||
試料 |
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キーワード | V-ATPase / SidK / rotational state 3 / HYDROLASE | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 vacuole-mitochondrion membrane contact site / protein localization to vacuolar membrane / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 ...vacuole-mitochondrion membrane contact site / protein localization to vacuolar membrane / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / P-type proton-exporting transporter activity / pexophagy / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / vacuolar proton-transporting V-type ATPase, V1 domain / protein targeting to vacuole / vacuole organization / cellular hyperosmotic response / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / fungal-type vacuole / intein-mediated protein splicing / intron homing / vacuolar acidification / phosphatidylinositol-3,5-bisphosphate binding / fungal-type vacuole membrane / proton transmembrane transporter activity / intracellular copper ion homeostasis / H+-transporting two-sector ATPase / ATP metabolic process / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / cell periphery / transmembrane transport / intracellular calcium ion homeostasis / cytoplasmic stress granule / endocytosis / ATPase binding / protein-containing complex assembly / endonuclease activity / intracellular iron ion homeostasis / 加水分解酵素; エステル加水分解酵素 / membrane raft / Golgi membrane / mRNA binding / ATP hydrolysis activity / DNA binding / ATP binding / membrane / cytoplasm 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / Legionella pneumophila subsp. pneumophila ATCC 43290 (バクテリア) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.6 Å | ||||||||||||||||||
データ登録者 | Zhao J | ||||||||||||||||||
資金援助 | カナダ, 米国, 5件
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引用 | ジャーナル: PLoS Pathog / 年: 2017 タイトル: Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein. 著者: Jianhua Zhao / Ksenia Beyrakhova / Yao Liu / Claudia P Alvarez / Stephanie A Bueler / Li Xu / Caishuang Xu / Michal T Boniecki / Voula Kanelis / Zhao-Qing Luo / Miroslaw Cygler / John L Rubinstein / 要旨: Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires' Disease, makes use of numerous effector ...Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires' Disease, makes use of numerous effector proteins to construct a niche supportive of its replication within phagocytic cells. The L. pneumophila effector SidK was identified in a screen for proteins that reduce the activity of the proton pumping vacuolar-type ATPases (V-ATPases) when expressed in the yeast Saccharomyces cerevisae. SidK is secreted by L. pneumophila in the early stages of infection and by binding to and inhibiting the V-ATPase, SidK reduces phagosomal acidification and promotes survival of the bacterium inside macrophages. We determined crystal structures of the N-terminal region of SidK at 2.3 Å resolution and used single particle electron cryomicroscopy (cryo-EM) to determine structures of V-ATPase:SidK complexes at ~6.8 Å resolution. SidK is a flexible and elongated protein composed of an α-helical region that interacts with subunit A of the V-ATPase and a second region of unknown function that is flexibly-tethered to the first. SidK binds V-ATPase strongly by interacting via two α-helical bundles at its N terminus with subunit A. In vitro activity assays show that SidK does not inhibit the V-ATPase completely, but reduces its activity by ~40%, consistent with the partial V-ATPase deficiency phenotype its expression causes in yeast. The cryo-EM analysis shows that SidK reduces the flexibility of the A-subunit that is in the 'open' conformation. Fluorescence experiments indicate that SidK binding decreases the affinity of V-ATPase for a fluorescent analogue of ATP. Together, these results reveal the structural basis for the fine-tuning of V-ATPase activity by SidK. | ||||||||||||||||||
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_8726.map.gz | 59.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8726-v30.xml emd-8726.xml | 32.9 KB 32.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_8726.png | 62.2 KB | ||
Filedesc metadata | emd-8726.cif.gz | 9.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8726 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8726 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8726_validation.pdf.gz | 563.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_8726_full_validation.pdf.gz | 563 KB | 表示 | |
XML形式データ | emd_8726_validation.xml.gz | 6.2 KB | 表示 | |
CIF形式データ | emd_8726_validation.cif.gz | 7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8726 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8726 | 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_8726.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | V-ATPase:SidK complex, rotational state 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.45 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
-試料の構成要素
+全体 : V-ATPase:SidK complex
+超分子 #1: V-ATPase:SidK complex
+超分子 #2: V-ATPase
+超分子 #3: SidK
+分子 #1: V-type proton ATPase catalytic subunit A,V-type proton ATPase cat...
+分子 #2: V-type proton ATPase subunit B
+分子 #3: V-type proton ATPase subunit E
+分子 #4: V-type proton ATPase subunit G
+分子 #5: V-type proton ATPase subunit D
+分子 #6: V-type proton ATPase subunit F
+分子 #7: V-type proton ATPase subunit C
+分子 #8: V-type proton ATPase subunit H
+分子 #9: V-type proton ATPase subunit d
+分子 #10: V-type proton ATPase subunit c''
+分子 #11: V-type proton ATPase subunit c'
+分子 #12: V-type proton ATPase subunit c
+分子 #13: V-type proton ATPase subunit a, vacuolar isoform
+分子 #14: V-type proton ATPase subunit e
+分子 #15: V-type proton ATPase subunit f
+分子 #16: Uncharacterized protein
-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
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE-PROPANE |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 1.2 e/Å2 |
電子線 | 加速電圧: 200 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 FIELD |
実験機器 | モデル: Tecnai F20 / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: EMDB MAP |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 7.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 13061 |
初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |