+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-44846 | |||||||||
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タイトル | V0-only V-ATPase and synaptophysin complex in mouse brain isolated synaptic vesicles | |||||||||
マップデータ | Half map A of V0-only V-ATPasesynaptophysin complex in wild-type ISVs. | |||||||||
試料 |
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キーワード | V0only V-ATPase / synaptic vesicle / MEMBRANE PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 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 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | |||||||||
データ登録者 | Wang C / Jiang W / Yang K / Wang X / Guo Q / Brunger AT | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nature / 年: 2024 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
添付画像 |
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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 | emd_44846.map.gz | 85.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-44846-v30.xml emd-44846.xml | 29.3 KB 29.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_44846.png | 157.2 KB | ||
Filedesc metadata | emd-44846.cif.gz | 8.1 KB | ||
その他 | emd_44846_additional_1.map.gz emd_44846_additional_2.map.gz emd_44846_half_map_1.map.gz emd_44846_half_map_2.map.gz | 84.4 MB 71.3 MB 84.5 MB 84.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-44846 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44846 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_44846_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_44846_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_44846_validation.xml.gz | 12.9 KB | 表示 | |
CIF形式データ | emd_44846_validation.cif.gz | 15.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44846 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44846 | HTTPS FTP |
-関連構造データ
関連構造データ | 9brzMC 9braC 9brqC 9brrC 9brsC 9brtC 9bruC 9bryC 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_44846.map.gz / 形式: CCP4 / 大きさ: 91.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Half map A of V0-only V-ATPasesynaptophysin complex in wild-type ISVs. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.111 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: #1
ファイル | emd_44846_additional_1.map | ||||||||||||
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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_44846_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 A of V0-only V-ATPasesynaptophysin complex in...
ファイル | emd_44846_half_map_1.map | ||||||||||||
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注釈 | Half map A of V0-only V-ATPasesynaptophysin complex in wild-type 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 B of V0-only V-ATPasesynaptophysin complex in...
ファイル | emd_44846_half_map_2.map | ||||||||||||
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注釈 | Half map B of V0-only V-ATPasesynaptophysin complex in wild-type ISVs. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Mouse brain isolated glutamatergic synaptic vesicles
+超分子 #1: Mouse brain isolated glutamatergic synaptic vesicles
+分子 #1: V-type proton ATPase subunit S1
+分子 #2: V-type proton ATPase 21 kDa proteolipid subunit c''
+分子 #3: V-type proton ATPase subunit d 1
+分子 #4: Ribonuclease kappa
+分子 #5: V-type proton ATPase 16 kDa proteolipid subunit c
+分子 #6: Renin receptor cytoplasmic fragment
+分子 #7: Synaptophysin
+分子 #8: V-type proton ATPase subunit e 2
+分子 #9: V-type proton ATPase 116 kDa subunit a 1
+分子 #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
-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 | cell |
-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. |
-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: FIELD EMISSION GUN |
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 |
-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: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 42137 |
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
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. |
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精密化 | プロトコル: FLEXIBLE FIT |
得られたモデル | PDB-9brz: |