EMDB-44355: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1

基本情報

登録情報

データベース: EMDB / ID: EMD-44355

• タイトル: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 1

試料

• 複合体: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3

• キーワード: Membrane / Complex / Native / Synaptic / PROTON TRANSPORT

機能・相同性

分子機能:

regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / regulation of synaptic vesicle priming / proton-transporting V-type ATPase, V1 domain / positive regulation of transforming growth factor beta1 production / transporter activator activity / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / extrinsic component of synaptic vesicle membrane / vacuolar transport / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / lysosomal lumen acidification / endosomal lumen acidification / neuron spine / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / osteoclast development / head morphogenesis / protein localization to cilium / regulation of short-term neuronal synaptic plasticity / vacuolar acidification / neuron projection terminus / dendritic spine membrane / regulation of cellular pH / syntaxin-1 binding / ROS and RNS production in phagocytes / Neutrophil degranulation / cholesterol binding / ATPase complex / response to amyloid-beta / ATPase activator activity / presynaptic active zone / microvillus / regulation of MAPK cascade / regulation of neuronal synaptic plasticity / autophagosome membrane / excitatory synapse / cilium assembly / positive regulation of Wnt signaling pathway / regulation of macroautophagy / ATP metabolic process / H+-transporting two-sector ATPase / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / ruffle / axon terminus / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / receptor-mediated endocytosis / SH2 domain binding / SNARE binding / secretory granule / modulation of chemical synaptic transmission / regulation of long-term neuronal synaptic plasticity / terminal bouton / neuromuscular junction / Schaffer collateral - CA1 synapse / small GTPase binding / transmembrane transport / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / apical part of cell / synaptic vesicle / melanosome / presynapse / signaling receptor activity / presynaptic membrane / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / early endosome / lysosome / positive regulation of ERK1 and ERK2 cascade / neuron projection / postsynaptic density / endosome / endosome membrane / cilium / apical plasma membrane / protein domain specific binding

ドメイン・相同性:

Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / Renin receptor-like transmembrane spanning segment / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / : / V-type proton ATPase subunit f-like / Ribonuclease kappa / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / ATPase, V1 complex, subunit D / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / ATP synthase (E/31 kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase

構成要素:

V-type proton ATPase subunit H / Rnasek protein / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit S1 / Synaptophysin / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / V-type proton ATPase subunit C 1 / V-type proton ATPase subunit / Type IV secretion protein Dot / Renin receptor / V-type proton ATPase subunit D / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit G

• 生物種: Rattus norvegicus (ドブネズミ)
• 手法: 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å
• データ登録者: Coupland CE / Rubinstein JL

資金援助

カナダ, 1件

Organization	Grant number	国
Canadian Institutes of Health Research (CIHR)	PJT166152	カナダ

• 引用: ジャーナル: Science / 年: 2024; タイトル: High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.; 著者: Claire E Coupland / Ryan Karimi / Stephanie A Bueler / Yingke Liang / Gautier M Courbon / Justin M Di Trani / Cassandra J Wong / Rayan Saghian / Ji-Young Youn / Lu-Yang Wang / John L Rubinstein / ; 要旨: Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single-particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in a loss of the V region of V-ATPase from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.

履歴

登録	2024年3月31日	-
ヘッダ(付随情報) 公開	2024年6月26日	-
マップ公開	2024年6月26日	-
更新	2024年7月24日	-
現状	2024年7月24日	処理サイト: RCSB / 状態: 公開

マップ

• ファイル: ダウンロード / ファイル: emd_44355.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• ボクセルのサイズ: X=Y=Z: 1.37333 Å

密度

表面レベル	登録者による: 0.19
最小 - 最大	-0.72986484 - 1.294984
平均 (標準偏差)	0.000119357544 (±0.03738775)

• 対称性: 空間群: 1

詳細

EMDB XML:

マップ形状	Axis order X Y Z Origin 0 0 0 サイズ 384 384 384 Spacing 384 384 384
セル	A=B=C: 527.36 Å α=β=γ: 90.0 °

添付データ

ハーフマップ: #2

• ファイル: emd_44355_half_map_1.map

ハーフマップ: #1

• ファイル: emd_44355_half_map_2.map

試料の構成要素

全体 : Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3

• 全体: 名称: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3

要素

• 複合体: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3

超分子 #1: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3

• 超分子: 名称: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3; タイプ: complex / ID: 1 / 親要素: 0
• 由来(天然): 生物種: Rattus norvegicus (ドブネズミ)

実験情報

構造解析

• 手法: クライオ電子顕微鏡法
• 解析: 単粒子再構成法
• 試料の集合状態: particle

試料調製

• 緩衝液: pH: 7.4
• 凍結: 凍結剤: ETHANE

電子顕微鏡法

• 顕微鏡: TFS KRIOS
• 撮影: フィルム・検出器のモデル: TFS FALCON 4i (4k x 4k); 平均電子線量: 37.5 e/Ų
• 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）: 1.9000000000000001 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: NONE
• 最終 再構成: 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 108773
• 初期 角度割当: タイプ: MAXIMUM LIKELIHOOD
• 最終 角度割当: タイプ: MAXIMUM LIKELIHOOD