+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8409 | |||||||||||||||
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タイトル | Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase | |||||||||||||||
マップデータ | Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase | |||||||||||||||
試料 |
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キーワード | Rotary ATPase / Vacuolar-type ATPase / Electron Cryomicroscopy / Vo region / Membrane protein / MOTOR PROTEIN | |||||||||||||||
機能・相同性 | 機能・相同性情報 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 ...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 / P-type proton-exporting transporter activity / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / 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 / vacuolar acidification / phosphatidylinositol-3,5-bisphosphate binding / fungal-type vacuole membrane / proton transmembrane transporter activity / intracellular copper ion homeostasis / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / membrane 類似検索 - 分子機能 | |||||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||||||||
データ登録者 | Mazhab-Jafari MT / Rohou A / Schmidt C / Bueler SA / Benlekbir S / Robinson CV / Rubinstein JL | |||||||||||||||
資金援助 | カナダ, 英国, European Union, 4件
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引用 | ジャーナル: Nature / 年: 2016 タイトル: Atomic model for the membrane-embedded V motor of a eukaryotic V-ATPase. 著者: Mohammad T Mazhab-Jafari / Alexis Rohou / Carla Schmidt / Stephanie A Bueler / Samir Benlekbir / Carol V Robinson / John L Rubinstein / 要旨: Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney ...Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V region drives proton translocation through the membrane-embedded V region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V and V regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the V complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits acc'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel. | |||||||||||||||
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_8409.map.gz | 27 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8409-v30.xml emd-8409.xml | 23.5 KB 23.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_8409.png | 149.9 KB | ||
Filedesc metadata | emd-8409.cif.gz | 7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8409 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8409 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8409_validation.pdf.gz | 519.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_8409_full_validation.pdf.gz | 519.4 KB | 表示 | |
XML形式データ | emd_8409_validation.xml.gz | 5.8 KB | 表示 | |
CIF形式データ | emd_8409_validation.cif.gz | 6.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8409 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8409 | 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_8409.map.gz / 形式: CCP4 / 大きさ: 30.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.554 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 : Vo region of the V-ATPase from Saccharomyces cerevisiae
全体 | 名称: Vo region of the V-ATPase from Saccharomyces cerevisiae |
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要素 |
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-超分子 #1: Vo region of the V-ATPase from Saccharomyces cerevisiae
超分子 | 名称: Vo region of the V-ATPase from Saccharomyces cerevisiae タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#8 |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
分子量 | 理論値: 300 KDa |
-分子 #1: V-type proton ATPase subunit a
分子 | 名称: V-type proton ATPase subunit a / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c |
分子量 | 理論値: 70.067984 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)AQYRE INAGLPTIVT FPFMFAIMFG DMGHG FLMT LAALSLVLNE KKINKMKRGE IFDMAFTGRY IILLMGVFSM YTGFLYNDIF SKTMTIFKSG WKWPDHWKKG ESITAT SVG TYPIGLDWAW HGTENALLFS NSYKMKLSIL MGFIHMTYSY FFSLANHLYF NSMIDIIGNF IPGLLFMQGI FGYLSVC IV YKWAVDWVKD GKPAPGLLNM LINMFLSPGT IDDELYPHQA KVQVFLLLMA LVCIPWLLLV KPLHFKFTHK KKSHEPLP S TEADASSEDL EAQQLISAMD ADDAEEEEVG SGSHGEDFGD IMIHQVIHTI EFCLNCVSHT ASYLRLWALS LAHAQLSSV LWTMTIQIAF GFRGFVGVFM TVALFAMWFA LTCAVLVLME GTSAMLHSLR LHWVESMSKF FVGEGLPYEP FAFEYKDMEV UniProtKB: V-type proton ATPase subunit a, vacuolar isoform |
-分子 #2: V-type proton ATPase subunit c''
分子 | 名称: V-type proton ATPase subunit c'' / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c |
分子量 | 理論値: 22.610641 KDa |
配列 | 文字列: MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA ...文字列: MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA TAAISDAADS ALFVKILVIE IFGSILGLLG LIVGLLMAGK ASEFQ UniProtKB: V-type proton ATPase subunit c'' |
-分子 #3: V-type proton ATPase subunit c'
分子 | 名称: V-type proton ATPase subunit c' / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c |
分子量 | 理論値: 15.195271 KDa |
配列 | 文字列: FFGFAGCAAA MVLSCLGAAI GTAKSGIGIA GIGTFKPELI MKSLIPVVMS GILAIYGLVV AVLIAGNLSP TEDYTLFNGF MHLSCGLCV GFACLSSGYA IGMVGDVGVR KYMHQPRLFV GIVLILIFSE VLGLYGMIVA LILNTRGS UniProtKB: V-type proton ATPase subunit c' |
-分子 #4: V-type proton ATPase subunit c
分子 | 名称: V-type proton ATPase subunit c / タイプ: protein_or_peptide / ID: 4 / コピー数: 8 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c |
分子量 | 理論値: 15.218087 KDa |
配列 | 文字列: APFFGAIGCA SAIIFTSLGA AYGTAKSGVG ICATCVLRPD LLFKNIVPVI MAGIIAIYGL VVSVLVCYSL GQKQALYTGF IQLGAGLSV GLSGLAAGFA IGIVGDAGVR GSSQQPRLFV GMILILIFAE VLGLYGLIVA LLLNSRATQD V UniProtKB: V-type proton ATPase subunit c |
-分子 #5: V-type proton ATPase subunit e
分子 | 名称: V-type proton ATPase subunit e / タイプ: protein_or_peptide / ID: 5 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c |
分子量 | 理論値: 6.476928 KDa |
配列 | 文字列: YTVVGVFIVV SAMSVLFWIM APKNNQAVWR STVILTLAMM FLMWAITFLC QLHPLVA UniProtKB: V-type proton ATPase subunit e |
-分子 #6: V-type proton ATPase subunit f
分子 | 名称: V-type proton ATPase subunit f / タイプ: protein_or_peptide / ID: 6 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c |
分子量 | 理論値: 4.613678 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-分子 #7: V-type proton ATPase subunit d
分子 | 名称: V-type proton ATPase subunit d / タイプ: protein_or_peptide / ID: 7 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 株: ATCC 204508 / S288c |
分子量 | 理論値: 32.854238 KDa |
配列 | 文字列: VYFNIDNGFI EGVVRGYRNG LLSNNQYINL TQCDTLEDLK LQLSSTDYGN FLSSVSSESL TTSLIQEYAS SKLYHEFNYI RDQSSGSTR KFMDYITYGY MIDNVALMIT GTIHDRDKGE ILQRCHPLGW FDTLPTLSVA TDLESLYETV LVD(UNK) (UNK)(UNK)(UNK) ...文字列: VYFNIDNGFI EGVVRGYRNG LLSNNQYINL TQCDTLEDLK LQLSSTDYGN FLSSVSSESL TTSLIQEYAS SKLYHEFNYI RDQSSGSTR KFMDYITYGY MIDNVALMIT GTIHDRDKGE ILQRCHPLGW FDTLPTLSVA TDLESLYETV LVD(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)NIEII RNKLYKAYLE DFYNFVTEEI P(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)LEDHF YQLEMELCRD AFTQQFAIST VWAWMKSKEQ EVRNITWIAE CIAQNQRERI NNY UniProtKB: V-type proton ATPase subunit d, V-type proton ATPase subunit d, V-type proton ATPase subunit d |
-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 | 2.5 mg/mL |
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緩衝液 | pH: 7.5 詳細: 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 micro M Bafilomycin |
グリッド | モデル: Maxtaform / 材質: COPPER/RHODIUM / メッシュ: 400 / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 15 sec. / 前処理 - 雰囲気: AIR |
凍結 | 凍結剤: ETHANE-PROPANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.3 K / 装置: FEI VITROBOT MARK III / 詳細: Modified for ethane/propane. |
詳細 | The Vo region was solubilized in amphipol A8-35 (Anatrace) |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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詳細 | 70 micro meter objective aperture, illuminated area of 1.58 micro meter diameter |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 撮影したグリッド数: 1 / 実像数: 4365 / 平均露光時間: 21.0 sec. / 平均電子線量: 100.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 最大 デフォーカス(補正後): 3.4 µm / 最小 デフォーカス(補正後): 0.8 µm / 倍率(補正後): 64350 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 倍率(公称値): 37000 |
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 |
+画像解析
-原子モデル構築 1
詳細 | phenix.real_space_refine REFINEMENT TARGET: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) MODEL TO MAP FIT. CC(ACROSS WHOLE MAP VOLUME): 0.6772 CC(ONLY ACROSS ATOMS IN THE MODEL): 0.6842 |
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精密化 | 空間: REAL / プロトコル: OTHER |
得られたモデル | PDB-5tj5: |