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基本情報
登録情報 | データベース: PDB / ID: 9brz | |||||||||
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タイトル | V0-only V-ATPase and synaptophysin complex in mouse brain isolated synaptic vesicles | |||||||||
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![]() | MEMBRANE PROTEIN / V0only V-ATPase / synaptic vesicle | |||||||||
機能・相同性 | ![]() Ion channel transport / regulation of opioid receptor signaling pathway / Amino acids regulate mTORC1 / clathrin-sculpted glutamate transport vesicle membrane / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / RHOA GTPase cycle / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins ...Ion channel transport / regulation of opioid receptor signaling pathway / Amino acids regulate mTORC1 / clathrin-sculpted glutamate transport vesicle membrane / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / RHOA GTPase cycle / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity / negative regulation of autophagic cell death / 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 / intracellular organelle / ROS and RNS production in phagocytes / proton-transporting V-type ATPase, V0 domain / P-type proton-exporting transporter activity / 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 / proton-transporting V-type ATPase complex / neuron spine / head morphogenesis / regulation of short-term neuronal synaptic plasticity / neuron projection terminus / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / syntaxin-1 binding / vacuolar acidification / osteoclast development / regulation of synaptic vesicle exocytosis / : / cholesterol binding / presynaptic active zone / regulation of neuronal synaptic plasticity / autophagosome membrane / regulation of MAPK cascade / ATPase activator activity / excitatory synapse / synaptic vesicle endocytosis / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / endomembrane system / axon terminus / proton transmembrane transport / RNA endonuclease activity / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / SH2 domain binding / SNARE binding / receptor-mediated endocytosis / regulation of long-term neuronal synaptic plasticity / Schaffer collateral - CA1 synapse / neuromuscular junction / terminal bouton / transmembrane transport / synaptic vesicle membrane / small GTPase binding / endocytosis / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / cell body / ATPase binding / chemical synaptic transmission / 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 / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome membrane / endosome / nuclear speck / neuron projection / apical plasma membrane / protein domain specific binding / lysosomal membrane / external side of plasma membrane / axon / centrosome / ubiquitin protein ligase binding / synapse / protein-containing complex binding 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: 3.8 Å | |||||||||
![]() | Wang, C. / Jiang, W. / Yang, K. / Wang, X. / Guo, Q. / Brunger, A.T. | |||||||||
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
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 | ![]() | 568.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 457.9 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 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2 MB | 表示 | |
XML形式データ | ![]() | 82.3 KB | 表示 | |
CIF形式データ | ![]() | 130 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 | ![]() 44846MC ![]() 9braC ![]() 9brqC ![]() 9brrC ![]() 9brsC ![]() 9brtC ![]() 9bruC ![]() 9bryC 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 | 類似検索 - 機能・相同性 ![]() |
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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 cbdghijklmnoea
#1: タンパク質 | 分子量: 51046.215 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: VAS1_MOUSE V-type proton ATPase subunit S1 / 由来: (天然) ![]() ![]() | ||||
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#2: タンパク質 | 分子量: 21618.553 Da / 分子数: 1 / 由来タイプ: 天然 詳細: VATO_MOUSE V-type proton ATPase 21 kDa proteolipid subunit 由来: (天然) ![]() ![]() | ||||
#3: タンパク質 | 分子量: 40341.934 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: VA0D1_MOUSE V-type proton ATPase subunit d 1 / 由来: (天然) ![]() ![]() | ||||
#5: タンパク質 | 分子量: 15815.833 Da / 分子数: 9 / 由来タイプ: 天然 詳細: VATL_MOUSE V-type proton ATPase 16 kDa proteolipid subunit 由来: (天然) ![]() ![]() #8: タンパク質 | | 分子量: 9203.020 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: VA0E2_MOUSE V-type proton ATPase subunit e 2 / 由来: (天然) ![]() ![]() #9: タンパク質 | | 分子量: 96442.500 Da / 分子数: 1 / 由来タイプ: 天然 詳細: VPP1_MOUSE V-type proton ATPase 116 kDa subunit a isoform 1 由来: (天然) ![]() ![]() |
-タンパク質 , 3種, 3分子 fps
#4: タンパク質 | 分子量: 11000.004 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: RNK_MOUSE Ribonuclease kappa / 由来: (天然) ![]() ![]() 参照: UniProt: Q8K3C0, 加水分解酵素; エステル加水分解酵素 |
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#6: タンパク質 | 分子量: 39128.789 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: RENR_MOUSE Renin receptor / 由来: (天然) ![]() ![]() |
#7: タンパク質 | 分子量: 34045.406 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: SYPH_MOUSE Synaptophysin / 由来: (天然) ![]() ![]() |
-糖 , 3種, 7分子 ![](data/chem/img/NAG.gif)
#10: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
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#11: 多糖 | #12: 糖 | |
-詳細
研究の焦点であるリガンドがあるか | N |
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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: CELL / 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: Mouse brain isolated glutamatergic synaptic vesicles タイプ: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#9 / 由来: NATURAL |
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分子量 | 実験値: NO |
由来(天然) | 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 詳細: The specimen state should be an intact subcellular component. |
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: TFS KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.21_5207: / 分類: 精密化 | |||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3次元再構成 | 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 42137 / 対称性のタイプ: POINT | |||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT 詳細: Initial model: 6VQH, 6WLW, mouse synaptophysin from AlphaFold2 . For fitting and refinement details, see https://doi.org/10.1038/s41586-024-07610-x. |