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基本情報
登録情報 | ![]() | |||||||||
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タイトル | Intact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles | |||||||||
![]() | Full map of V-ATPase State 2 in synaptophysin knock-out ISVs. | |||||||||
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![]() | V-ATPase / synaptic vesicle / MEMBRANE PROTEIN | |||||||||
機能・相同性 | ![]() Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / eye pigmentation / Insulin receptor recycling / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / RHOA GTPase cycle / rostrocaudal neural tube patterning ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / eye pigmentation / Insulin receptor recycling / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / RHOA GTPase cycle / rostrocaudal neural tube patterning / Metabolism of Angiotensinogen to Angiotensins / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / ROS and RNS production in phagocytes / intracellular organelle / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar transport / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / protein localization to cilium / vacuolar acidification / dendritic spine membrane / regulation of cellular pH / osteoclast development / ATPase complex / autophagosome membrane / microvillus / regulation of MAPK cascade / ATPase activator activity / transmembrane transporter complex / positive regulation of Wnt signaling pathway / cilium assembly / angiotensin maturation / regulation of macroautophagy / endomembrane system / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / phagocytic vesicle / RNA endonuclease activity / ruffle / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule / transmembrane transport / cilium / synaptic vesicle membrane / small GTPase binding / endocytosis / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / apical part of cell / myelin sheath / signaling receptor activity / cell body / 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 / early endosome / positive regulation of ERK1 and ERK2 cascade / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / centrosome / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / nucleoplasm / ATP binding / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.4 Å | |||||||||
![]() | Wang C / Jiang W / Yang K / Wang X / Guo Q / Brunger AT | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure and topography of the synaptic V-ATPase-synaptophysin complex. 著者: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang / ...著者: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang / Michael H B Stowell / Wolfgang Baumeister / Qiang Guo / Axel T Brunger / ![]() ![]() ![]() 要旨: Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here, we discovered a ...Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here, we discovered a well-defined interface between the synaptic vesicle V-ATPase and synaptophysin by in situ cryo-electron tomography and single particle cryo-electron microscopy of functional synaptic vesicles isolated from mouse brains. The synaptic vesicle V-ATPase is an ATP-dependent proton pump that establishes the protein gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogs synaptoporin and synaptogyrin belong to a family of abundant synaptic vesicle proteins whose function is still unclear. We performed structural and functional studies of synaptophysin knockout mice, confirming the identity of synaptophysin as an interaction partner with the V-ATPase. Although there is little change in the conformation of the V-ATPase upon interaction with synaptophysin, the presence of synaptophysin in synaptic vesicles profoundly affects the copy number of V-ATPases. This effect on the topography of synaptic vesicles suggests that synaptophysin assists in their biogenesis. In support of this model, we observed that synaptophysin knockout mice exhibit severe seizure susceptibility, suggesting an imbalance of neurotransmitter release as a physiological consequence of the absence of synaptophysin. | |||||||||
履歴 |
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構造の表示
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 321.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 37.8 KB 37.8 KB | 表示 表示 | ![]() |
画像 | ![]() | 118.2 KB | ||
Filedesc metadata | ![]() | 9.7 KB | ||
その他 | ![]() ![]() ![]() ![]() | 318.4 MB 274.4 MB 274.1 MB 274.3 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 16.6 KB | 表示 | |
CIF形式データ | ![]() | 19.5 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 | ![]() 9brsMC ![]() 9braC ![]() 9brqC ![]() 9brrC ![]() 9brtC ![]() 9bruC ![]() 9bryC ![]() 9brzC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||
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注釈 | Full map of V-ATPase State 2 in synaptophysin knock-out ISVs. | ||||||||||||||||||||||||||||||||||||
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: 1.1064 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: EMhancer map of V-ATPase State 2 in synaptophysin knock-out ISVs.
ファイル | emd_44842_additional_1.map | ||||||||||||
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注釈 | EMhancer map of V-ATPase State 2 in synaptophysin knock-out ISVs. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unsharpened map
ファイル | emd_44842_additional_2.map | ||||||||||||
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注釈 | Unsharpened map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map of V-ATPase State 2 in synaptophysin knock-out ISVs.
ファイル | emd_44842_half_map_1.map | ||||||||||||
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注釈 | Half map of V-ATPase State 2 in synaptophysin knock-out ISVs. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map of V-ATPase State 2 in synaptophysin knock-out ISVs.
ファイル | emd_44842_half_map_2.map | ||||||||||||
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注釈 | Half map of V-ATPase State 2 in synaptophysin knock-out ISVs. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Synaptophysin knock-out mouse brain isolated glutamatergic synapt...
+超分子 #1: Synaptophysin knock-out mouse brain isolated glutamatergic synapt...
+分子 #1: V-type proton ATPase subunit E 1
+分子 #2: V-type proton ATPase subunit G 2
+分子 #3: V-type proton ATPase subunit C 1
+分子 #4: V-type proton ATPase subunit H
+分子 #5: V-type proton ATPase 116 kDa subunit a 1
+分子 #6: V-type proton ATPase subunit e 2
+分子 #7: Ribonuclease kappa
+分子 #8: V-type proton ATPase subunit F
+分子 #9: V-type proton ATPase subunit d 1
+分子 #10: V-type proton ATPase subunit S1
+分子 #11: Renin receptor cytoplasmic fragment
+分子 #12: V-type proton ATPase 21 kDa proteolipid subunit c''
+分子 #13: V-type proton ATPase 16 kDa proteolipid subunit c
+分子 #14: V-type proton ATPase catalytic subunit A
+分子 #15: V-type proton ATPase subunit B, brain isoform
+分子 #16: 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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![]() | 単粒子再構成法 |
試料の集合状態 | cell |
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試料調製
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE |
詳細 | The specimen state should be an intact subcellular component. |
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電子顕微鏡法
顕微鏡 | TFS KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: OTHER |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 30487 |
初期 角度割当 | タイプ: RANDOM ASSIGNMENT |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
-原子モデル構築 1
精密化 | プロトコル: FLEXIBLE FIT |
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得られたモデル | ![]() PDB-9brs: |