+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0648 | |||||||||
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タイトル | Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3 | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Proton pump / MEMBRANE PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly ...vacuole-mitochondrion membrane contact site / cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / proton-transporting V-type ATPase, V1 domain / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / proteasome storage granule assembly / P-type proton-exporting transporter activity / plasma membrane proton-transporting V-type ATPase complex / pexophagy / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / vacuole organization / protein targeting to vacuole / proton-transporting V-type ATPase complex / fungal-type vacuole / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-4-phosphate binding / vacuolar acidification / proton transmembrane transporter activity / intracellular copper ion homeostasis / endomembrane system / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / Neutrophil degranulation / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / cell periphery / transmembrane transport / cytoplasmic stress granule / intracellular calcium ion homeostasis / endocytosis / late endosome / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / early endosome / endosome membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / ATP hydrolysis activity / ATP binding / membrane / cytoplasm 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) / Saccharomyces cerevisiae (strain RM11-1a) (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: 8.7 Å | |||||||||
データ登録者 | Vasanthakumar T / Bueler SA / Wu D / Beilsten-Edmands V / Robinson CV / Rubinstein JL | |||||||||
資金援助 | カナダ, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2019 タイトル: Structural comparison of the vacuolar and Golgi V-ATPases from . 著者: Thamiya Vasanthakumar / Stephanie A Bueler / Di Wu / Victoria Beilsten-Edmands / Carol V Robinson / John L Rubinstein / 要旨: Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal ...Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast , isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that V complexes containing Stv1p could be readily purified without attached V regions. We used this effect to determine structures of the membrane-embedded V region with Stv1p at 3.1-Å resolution, which we compare with a structure of the V region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring. | |||||||||
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_0648.map.gz | 31 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0648-v30.xml emd-0648.xml | 28.8 KB 28.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0648.png | 26.8 KB | ||
Filedesc metadata | emd-0648.cif.gz | 8.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0648 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0648 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0648_validation.pdf.gz | 431.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0648_full_validation.pdf.gz | 430.7 KB | 表示 | |
XML形式データ | emd_0648_validation.xml.gz | 6.4 KB | 表示 | |
CIF形式データ | emd_0648_validation.cif.gz | 7.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0648 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0648 | 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_0648.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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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 : Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3
+超分子 #1: Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3
+分子 #1: V-type proton ATPase subunit C
+分子 #2: V-type proton ATPase subunit D
+分子 #3: V-type proton ATPase subunit F
+分子 #4: Vacuolar ATP synthase catalytic subunit A
+分子 #5: V-type proton ATPase subunit B
+分子 #6: V-type proton ATPase subunit G
+分子 #7: V-type proton ATPase subunit E
+分子 #8: V-type proton ATPase subunit H
+分子 #9: V-type proton ATPase subunit a, Golgi isoform
+分子 #10: V0 assembly protein 1
+分子 #11: V-type proton ATPase subunit c''
+分子 #12: V-type proton ATPase subunit d
+分子 #13: V-type proton ATPase subunit c
+分子 #14: V-type proton ATPase subunit c'
+分子 #15: V-type proton ATPase subunit e
+分子 #16: Putative protein YPR170W-B
-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: 7.4 |
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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: 35.0 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: OTHER / 詳細: Ab initio |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 8.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 7283 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |