+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-44840 | |||||||||
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タイトル | Intact V-ATPase State 3 and synaptophysin complex in mouse brain isolated synaptic vesicles | |||||||||
マップデータ | Full map of V-ATPase State 3 synaptophysin complex in wild-type ISVs. | |||||||||
試料 |
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キーワード | 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 / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / regulation of synaptic vesicle priming / 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 / intracellular organelle / ROS and RNS production in phagocytes / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / endosome to plasma membrane protein transport / lysosomal lumen acidification / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / proton-transporting V-type ATPase complex / neuron spine / head morphogenesis / osteoclast development / protein localization to cilium / 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 / cholesterol binding / : / ATPase complex / regulation of neuronal synaptic plasticity / presynaptic active zone / microvillus / autophagosome membrane / regulation of MAPK cascade / ATPase activator activity / synaptic vesicle endocytosis / excitatory synapse / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / endomembrane system / regulation of macroautophagy / angiotensin maturation / ATP metabolic process / axon terminus / H+-transporting two-sector ATPase / ruffle / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / proton transmembrane transport / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / SH2 domain binding / receptor-mediated endocytosis / SNARE binding / secretory granule / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / neuromuscular junction / Schaffer collateral - CA1 synapse / terminal bouton / cilium / transmembrane transport / small GTPase binding / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / endocytosis / melanosome / synaptic vesicle / apical part of cell / myelin sheath / ATPase binding / presynapse / signaling receptor activity / presynaptic membrane / cell body / chemical synaptic transmission / postsynaptic membrane / intracellular iron ion homeostasis / positive regulation of ERK1 and ERK2 cascade / endosome / receptor-mediated endocytosis of virus by host cell 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: 4.3 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 G 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 G 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 proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogues 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_44840.map.gz | 322 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-44840-v30.xml emd-44840.xml | 38.9 KB 38.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_44840.png | 152.9 KB | ||
Filedesc metadata | emd-44840.cif.gz | 9.9 KB | ||
その他 | emd_44840_additional_1.map.gz emd_44840_additional_2.map.gz emd_44840_half_map_1.map.gz emd_44840_half_map_2.map.gz | 319.3 MB 273.8 MB 318 MB 318 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-44840 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44840 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_44840_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_44840_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_44840_validation.xml.gz | 16.9 KB | 表示 | |
CIF形式データ | emd_44840_validation.cif.gz | 19.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44840 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44840 | HTTPS FTP |
-関連構造データ
関連構造データ | 9brqMC 9braC 9brrC 9brsC 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 (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_44840.map.gz / 形式: CCP4 / 大きさ: 343 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Full map of V-ATPase State 3 synaptophysin complex in wild-type ISVs. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.11138 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 3 synaptophysin complex...
ファイル | emd_44840_additional_1.map | ||||||||||||
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注釈 | EMhancer map of V-ATPase State 3 synaptophysin complex in wild-type 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 of V-ATPase State 3
ファイル | emd_44840_additional_2.map | ||||||||||||
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注釈 | Unsharpened map of V-ATPase State 3 | ||||||||||||
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 3 synaptophysin complex in wild-type ISVs.
ファイル | emd_44840_half_map_1.map | ||||||||||||
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注釈 | Half map of V-ATPase State 3 synaptophysin 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 of V-ATPase State 3 synaptophysin complex in wild-type ISVs.
ファイル | emd_44840_half_map_2.map | ||||||||||||
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注釈 | Half map of V-ATPase State 3 synaptophysin 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 21 kDa proteolipid subunit c''
+分子 #2: V-type proton ATPase 16 kDa proteolipid subunit c
+分子 #3: V-type proton ATPase catalytic subunit A
+分子 #4: V-type proton ATPase subunit B, brain isoform
+分子 #5: V-type proton ATPase subunit D
+分子 #6: V-type proton ATPase subunit E 1
+分子 #7: V-type proton ATPase subunit G 2
+分子 #8: V-type proton ATPase subunit F
+分子 #9: V-type proton ATPase subunit C 1
+分子 #10: V-type proton ATPase subunit H
+分子 #11: V-type proton ATPase subunit d 1
+分子 #12: V-type proton ATPase 116 kDa subunit a 1
+分子 #13: V-type proton ATPase subunit S1
+分子 #14: Renin receptor cytoplasmic fragment
+分子 #15: Ribonuclease kappa
+分子 #16: Synaptophysin
+分子 #17: V-type proton ATPase subunit e 2
-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): 4.0 µm / 最小 デフォーカス(公称値): 1.0 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: 4.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 34536 |
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-9brq: |