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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: 6wlw | ||||||
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タイトル | The Vo region of human V-ATPase in state 1 (focused refinement) | ||||||
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![]() | MEMBRANE PROTEIN / V-ATPase / proton pump | ||||||
機能・相同性 | ![]() proton-transporting two-sector ATPase complex / Ion channel transport / intracellular pH reduction / eye pigmentation / central nervous system maturation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production ...proton-transporting two-sector ATPase complex / Ion channel transport / intracellular pH reduction / eye pigmentation / central nervous system maturation / transporter activator activity / ATPase-coupled ion transmembrane transporter activity / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / Golgi lumen acidification / proton-transporting V-type ATPase, V0 domain / Transferrin endocytosis and recycling / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / XBP1(S) activates chaperone genes / Amino acids regulate mTORC1 / proton-transporting V-type ATPase complex / head morphogenesis / ROS and RNS production in phagocytes / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / osteoclast development / azurophil granule membrane / autophagosome membrane / regulation of MAPK cascade / tertiary granule membrane / ATPase activator activity / ficolin-1-rich granule membrane / positive regulation of Wnt signaling pathway / cilium assembly / RHOA GTPase cycle / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / axon terminus / proton transmembrane transport / Insulin receptor recycling / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule membrane / transmembrane transport / synaptic vesicle membrane / small GTPase binding / phagocytic vesicle membrane / melanosome / positive regulation of canonical Wnt signaling pathway / signaling receptor activity / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / 加水分解酵素; エステル加水分解酵素 / lysosome / early endosome / endosome membrane / nuclear speck / apical plasma membrane / lysosomal membrane / external side of plasma membrane / axon / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol 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 Å | ||||||
![]() | Wang, L. / Wu, H. / Fu, T.-M. | ||||||
![]() | ![]() タイトル: Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. 著者: Longfei Wang / Di Wu / Carol V Robinson / Hao Wu / Tian-Min Fu / ![]() ![]() 要旨: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton ...Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V complex for ATP hydrolysis and a membrane-embedded V complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the V complex. We define ATP6AP1 as a structural hub for V complex assembly because it connects to multiple V subunits and phospholipids in the c-ring. The glycolipids and the glycosylated V subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids. | ||||||
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 503.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 420.7 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 2.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.3 MB | 表示 | |
XML形式データ | ![]() | 85.6 KB | 表示 | |
CIF形式データ | ![]() | 120.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 21844MC ![]() 6wlzC ![]() 6wm2C ![]() 6wm3C ![]() 6wm4C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data #1: Unaligned multi frame micrographs of human V-ATPase in complex with SidK [micrographs - multiframe]) |
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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
-V-type proton ATPase ... , 6種, 14分子 0123456789QRSU
#1: タンパク質 | 分子量: 21418.213 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() | ||||||||
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#2: タンパク質 | 分子量: 15743.655 Da / 分子数: 9 / 由来タイプ: 天然 / 由来: (天然) ![]() #3: タンパク質 | | 分子量: 40369.949 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() #4: タンパク質 | | 分子量: 96512.414 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() #5: タンパク質 | | 分子量: 9380.329 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() #7: タンパク質 | | 分子量: 52067.480 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-タンパク質 , 2種, 2分子 TV
#6: タンパク質 | 分子量: 15435.220 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() 参照: UniProt: Q6P5S7, 加水分解酵素; エステル加水分解酵素 |
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#8: タンパク質 | 分子量: 39045.855 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-糖 , 5種, 9分子 ![](data/chem/img/NAG.gif)
#9: 多糖 | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | ||||
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#10: 多糖 | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose | ||||
#11: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #12: 多糖 | alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D- ...alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #19: 糖 | ChemComp-NAG / | |
-非ポリマー , 6種, 30分子 ![](data/chem/img/WSS.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/WJS.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/PSF.gif)
![](data/chem/img/WJP.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/WJS.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/PSF.gif)
![](data/chem/img/WJP.gif)
#13: 化合物 | ChemComp-WSS / #14: 化合物 | ChemComp-PTY / #15: 化合物 | ChemComp-WJS / ( | #16: 化合物 | ChemComp-CLR / #17: 化合物 | ChemComp-PSF / | #18: 化合物 | ChemComp-WJP / | |
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-詳細
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: Human V-ATPase with SidK / タイプ: COMPLEX / Entity ID: #1-#8 / 由来: RECOMBINANT |
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由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() |
緩衝液 | pH: 7.4 |
試料 | 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: 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: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 50.1 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.17.1_3660: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 1000000 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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