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基本情報
登録情報 | データベース: PDB / ID: 6mti | ||||||
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タイトル | Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+ | ||||||
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![]() | EXOCYTOSIS / SNARE / lipid nanotubes | ||||||
機能・相同性 | ![]() trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling ...trans-Golgi Network Vesicle Budding / BLOC-1 complex / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / calcium-dependent activation of synaptic vesicle fusion / calcium ion sensor activity / regulation of regulated secretory pathway / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / spontaneous neurotransmitter secretion / Lysosome Vesicle Biogenesis / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / zymogen granule membrane / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / regulated exocytosis / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / regulation of establishment of protein localization / storage vacuole / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / eosinophil degranulation / vesicle fusion / regulation of calcium ion-dependent exocytosis / vesicle docking / positive regulation of calcium ion-dependent exocytosis / exocytic vesicle / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of intracellular protein transport / positive regulation of dendrite extension / Golgi to plasma membrane protein transport / regulation of exocytosis / positive regulation of hormone secretion / neurotransmitter secretion / neurotransmitter receptor internalization / protein localization to membrane / calcium-dependent phospholipid binding / ATP-dependent protein binding / neuron projection terminus / neurotransmitter transport / regulation of synaptic vesicle recycling / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / clathrin-coated vesicle / synaptic vesicle priming / Neutrophil degranulation / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / regulation of synaptic vesicle exocytosis / low-density lipoprotein particle receptor binding / clathrin binding / myosin binding / regulation of dopamine secretion / exocytosis / phosphatidylserine binding / voltage-gated potassium channel activity / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / associative learning / positive regulation of excitatory postsynaptic potential / protein sumoylation 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 10.4 Å | ||||||
![]() | Grushin, K. / Wang, J. / Coleman, J. / Rothman, J. / Sindelar, C. / Krishnakumar, S. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural basis for the clamping and Ca activation of SNARE-mediated fusion by synaptotagmin. 著者: Kirill Grushin / Jing Wang / Jeff Coleman / James E Rothman / Charles V Sindelar / Shyam S Krishnakumar / ![]() ![]() 要旨: Synapotagmin-1 (Syt1) interacts with both SNARE proteins and lipid membranes to synchronize neurotransmitter release to calcium (Ca) influx. Here we report the cryo-electron microscopy structure of ...Synapotagmin-1 (Syt1) interacts with both SNARE proteins and lipid membranes to synchronize neurotransmitter release to calcium (Ca) influx. Here we report the cryo-electron microscopy structure of the Syt1-SNARE complex on anionic-lipid containing membranes. Under resting conditions, the Syt1 C2 domains bind the membrane with a magnesium (Mg)-mediated partial insertion of the aliphatic loops, alongside weak interactions with the anionic lipid headgroups. The C2B domain concurrently interacts the SNARE bundle via the 'primary' interface and is positioned between the SNAREpins and the membrane. In this configuration, Syt1 is projected to sterically delay the complete assembly of the associated SNAREpins and thus, contribute to clamping fusion. This Syt1-SNARE organization is disrupted upon Ca-influx as Syt1 reorients into the membrane, likely displacing the attached SNAREpins and reversing the fusion clamp. We thus conclude that the cation (Mg/Ca) dependent membrane interaction is a key determinant of the dual clamp/activator function of Synaptotagmin-1. | ||||||
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構造ビューア | 分子: ![]() ![]() |
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-検証レポート
文書・要旨 | ![]() | 1.6 MB | 表示 | ![]() |
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-関連構造データ
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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
-Synaptotagmin- ... , 2種, 6分子 162345
#1: タンパク質 | 分子量: 14654.769 Da / 分子数: 2 / 断片: C2A domain, residues 141-267 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #2: タンパク質 | 分子量: 32247.197 Da / 分子数: 4 / 断片: C2A and C2B domains, residues 141-421 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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-タンパク質 , 2種, 12分子 AEIMQUBFJNRV
#3: タンパク質 | 分子量: 7231.061 Da / 分子数: 6 / 断片: residues 28-89 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #4: タンパク質 | 分子量: 7837.957 Da / 分子数: 6 / 断片: residues 191-256 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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-Synaptosomal-associated protein ... , 2種, 12分子 CGKOSWDHLPTX
#5: タンパク質 | 分子量: 9030.114 Da / 分子数: 6 / 断片: residues 7-83 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #6: タンパク質 | 分子量: 7471.368 Da / 分子数: 6 / 断片: residues 141-204 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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-非ポリマー , 1種, 10分子 ![](data/chem/img/MG.gif)
#7: 化合物 | ChemComp-MG / |
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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: HELICAL ARRAY / 3次元再構成法: らせん対称体再構成法 |
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試料調製
構成要素 | 名称: Synaptotagmin-1 C2A and C2B domains in the complex with SNARE proteins on the surface of lipid membrane nanotube タイプ: COMPLEX / Entity ID: #1-#6 / 由来: RECOMBINANT |
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由来(天然) | 生物種: ![]() ![]() |
由来(組換発現) | 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 |
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: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 44 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
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解析
EMソフトウェア | 名称: Situs / カテゴリ: モデルフィッティング |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
らせん対称 | 回転角度/サブユニット: 78.48 ° / 軸方向距離/サブユニット: 7.3 Å / らせん対称軸の対称性: C1 |
3次元再構成 | 解像度: 10.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 2082 / 対称性のタイプ: HELICAL |
原子モデル構築 | プロトコル: RIGID BODY FIT |
原子モデル構築 | PDB-ID: 5CCI Accession code: 5CCI / Source name: PDB / タイプ: experimental model |