+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2n1t | ||||||
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タイトル | Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution | ||||||
要素 |
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キーワード | EXOCYTOSIS (エキソサイトーシス) / Synaptotagmin-1 / C2B domain / Syntaxin-1A / Synaptobrevin-2 / SNAP-25 (SNAP25) / SNAP-25A / SNARE complex | ||||||
機能・相同性 | 機能・相同性情報 Toxicity of botulinum toxin type C (botC) / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / trans-Golgi Network Vesicle Budding / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter ...Toxicity of botulinum toxin type C (botC) / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / neurotransmitter uptake / Toxicity of botulinum toxin type G (botG) / trans-Golgi Network Vesicle Budding / 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 / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / calcium-dependent activation of synaptic vesicle fusion / Acetylcholine Neurotransmitter Release Cycle / regulation of regulated secretory pathway / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Toxicity of botulinum toxin type A (botA) / calcium ion sensor activity / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / Lysosome Vesicle Biogenesis / regulation of synaptic vesicle priming / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / zymogen granule membrane / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / chromaffin granule membrane / regulated exocytosis / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / storage vacuole / response to gravity / calcium ion-regulated exocytosis of neurotransmitter / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / eosinophil degranulation / 小胞融合 / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / positive regulation of calcium ion-dependent exocytosis / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / chloride channel inhibitor activity / secretion by cell / SNARE complex / Golgi to plasma membrane protein transport / SNAP receptor activity / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / Cargo recognition for clathrin-mediated endocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / ミオフィラメント / positive regulation of intracellular protein transport / positive regulation of dendrite extension / regulation of exocytosis / neurotransmitter secretion / neurotransmitter receptor internalization / calcium-dependent phospholipid binding / ATP-dependent protein binding / neuron projection terminus / protein localization to membrane / 神経伝達物質輸送体 / regulation of synaptic vesicle recycling / Neurexins and neuroligins / insulin secretion / Sensory processing of sound by inner hair cells of the cochlea / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / クラスリン / synaptic vesicle priming / regulation of neuron projection development / regulation of synapse assembly / endosomal transport / low-density lipoprotein particle receptor binding 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) Homo sapiens (ヒト) | ||||||
手法 | 溶液NMR / molecular dynamics | ||||||
データ登録者 | Brewer, K. / Bacaj, T. / Cavalli, A. / Camilloni, C. / Swarbrick, J. / Liu, J. / Zhou, A. / Zhou, P. / Barlow, N. / Xu, J. ...Brewer, K. / Bacaj, T. / Cavalli, A. / Camilloni, C. / Swarbrick, J. / Liu, J. / Zhou, A. / Zhou, P. / Barlow, N. / Xu, J. / Seven, A. / Prinslow, E. / Voleti, R. / Haussinger, D. / Bonvin, A. / Tomchick, D. / Vendruscolo, M. / Graham, B. / Sudhof, T. / Rizo, J. | ||||||
引用 | ジャーナル: Nat.Struct.Mol.Biol. / 年: 2015 タイトル: Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution. 著者: Brewer, K.D. / Bacaj, T. / Cavalli, A. / Camilloni, C. / Swarbrick, J.D. / Liu, J. / Zhou, A. / Zhou, P. / Barlow, N. / Xu, J. / Seven, A.B. / Prinslow, E.A. / Voleti, R. / Haussinger, D. / ...著者: Brewer, K.D. / Bacaj, T. / Cavalli, A. / Camilloni, C. / Swarbrick, J.D. / Liu, J. / Zhou, A. / Zhou, P. / Barlow, N. / Xu, J. / Seven, A.B. / Prinslow, E.A. / Voleti, R. / Haussinger, D. / Bonvin, A.M. / Tomchick, D.R. / Vendruscolo, M. / Graham, B. / Sudhof, T.C. / Rizo, J. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 2n1t.cif.gz | 712.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2n1t.ent.gz | 599.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2n1t.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/n1/2n1t ftp://data.pdbj.org/pub/pdb/validation_reports/n1/2n1t | HTTPS FTP |
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-関連構造データ
関連構造データ | |
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類似構造データ | |
その他のデータベース |
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-リンク
-集合体
登録構造単位 |
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NMR アンサンブル |
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-要素
#1: タンパク質 | 分子量: 8045.023 Da / 分子数: 1 / 断片: UNP residues 25-93 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Syb2, Vamp2 / プラスミド: pGEX-KT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63045 |
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#2: タンパク質 | 分子量: 8429.528 Da / 分子数: 1 / 断片: UNP residues 188-259 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Sap, Stx1a / プラスミド: pGEX-KT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P32851 |
#3: タンパク質 | 分子量: 9030.114 Da / 分子数: 1 / 断片: N-terminal domain (UNP residues 7-83) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNAP, SNAP25, SNAP-25A / プラスミド: pGEX-KT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P60880 |
#4: タンパク質 | 分子量: 8458.420 Da / 分子数: 1 / 断片: C-terminal domain (UNP residues 131-204) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SNAP, SNAP25, SNAP-25A / プラスミド: pGEX-KT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P60880 |
#5: タンパク質 | 分子量: 17465.236 Da / 分子数: 1 / 断片: C2B domain (UNP residues 272-419) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SVP65, SYT, SYT1 / プラスミド: pGEX-KT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P21579 |
構成要素の詳細 | RESIDUE ASP 41 OF SNAP-25 N-TERMINAL DOMAIN (CHAIN C) WAS MUTATED TO CYS, AND LABELED WITH DY-C2 ...RESIDUE ASP 41 OF SNAP-25 N-TERMINAL DOMAIN (CHAIN C) WAS MUTATED TO CYS, AND LABELED WITH DY-C2 TAG IN SOME SAMPLES. |
配列の詳細 | THE SEQUENCES OF CHAIN C AND D MATCH ISOFORM 2 SEQUENCE WITH UNIPROT IDENTIFIER |
-実験情報
-実験
実験 | 手法: 溶液NMR 詳細: This deposition includes five conformers of the synaptotagmin-1 C2B domain SNARE complex. This complex is highly dynamic under the solution conditions used in the measurement of pseudocontact ...詳細: This deposition includes five conformers of the synaptotagmin-1 C2B domain SNARE complex. This complex is highly dynamic under the solution conditions used in the measurement of pseudocontact shifts by NMR spectroscopy that provided the structural information for this analysis. Because of this highly dynamic nature, no single structure can be considered as 'the structure' of this complex under our conditions. The five conformers deposited must be considered as just a few of the many conformers that form the ensemble but illustrate the types of interactions between the synaptotagmin-1 C2B domain and the SNARE complex that mediate this dynamic binding mode. | ||||||||||||
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NMR実験 |
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-試料調製
詳細 | タイプ: solution 内容: 30 uM [U-100% 13C; U-100% 15N] protein, 25 mM Tris-HCl, 125 mM KSCN, 1 mM CaCl2, 90% H2O/10% D2O Label: sample_1 / 溶媒系: 90% H2O/10% D2O | ||||||||||||||||||||
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試料 |
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試料状態 | pH: 7.4 / 圧: ambient / 温度: 298 K |
-NMR測定
NMRスペクトロメーター |
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-解析
NMR software |
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精密化 | 手法: molecular dynamics / ソフトェア番号: 3 詳細: MOLECULAR DYNAMICS SIMULATIONS WERE USED TO GENERATE STRUCTURES OF THE SYNAPTOTAGMIN-1 C2B DOMAIN-SNARE COMPLEX THAT COULD BE EVALUATED BASED ON HOW WELL THEY FIT THE MEASURED PSEUDOCONTACT ...詳細: MOLECULAR DYNAMICS SIMULATIONS WERE USED TO GENERATE STRUCTURES OF THE SYNAPTOTAGMIN-1 C2B DOMAIN-SNARE COMPLEX THAT COULD BE EVALUATED BASED ON HOW WELL THEY FIT THE MEASURED PSEUDOCONTACT SHIFTS. SINCE IT WAS CLEAR FROM THE ANALYSIS THAT THE COMPLEX IS HIGHLY DYNAMICS AND NO SINGLE STRUCTURE CAN FIT ALL THE DATA, THE STRUCTURES FROM THE SIMULATIONS WERE USED TO TRY TO FIT THE MEASURED PSEUDOCONTACT SHIFTS AS ENSEMBLED-AVERAGED VALUES. THE STRUCTURES IN THE DEPOSITION ARE AMONG THOSE THAT CONTRIBUTED TO THE BEST ENSEMBLE-AVERAGE FITS. | ||||||||||||||||||||||||||||
代表構造 | 選択基準: all these conformers contribute to this dynamics ensemble | ||||||||||||||||||||||||||||
NMRアンサンブル | コンフォーマー選択の基準: Contribution to fit PCS data 計算したコンフォーマーの数: 10000 / 登録したコンフォーマーの数: 5 |