+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6mdm | ||||||
---|---|---|---|---|---|---|---|
タイトル | The 20S supercomplex engaging the SNAP-25 N-terminus (class 1) | ||||||
要素 |
| ||||||
キーワード | HYDROLASE / SNARE / NSF / SNAP / ATPase / AAA / disassembly / synapse / membrane fusion / exocytosis | ||||||
機能・相同性 | 機能・相同性情報 soluble NSF attachment protein activity / Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / trans-Golgi Network Vesicle Budding / BLOC-1 complex / SNARE complex disassembly / regulation of delayed rectifier potassium channel activity / myosin head/neck binding ...soluble NSF attachment protein activity / Intra-Golgi traffic / Retrograde transport at the Trans-Golgi-Network / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / trans-Golgi Network Vesicle Budding / BLOC-1 complex / SNARE complex disassembly / regulation of delayed rectifier potassium channel activity / myosin head/neck binding / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Other interleukin signaling / ribbon synapse / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / extrinsic component of presynaptic membrane / Lysosome Vesicle Biogenesis / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / positive regulation of norepinephrine secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / COPII-mediated vesicle transport / positive regulation of catecholamine secretion / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / protein-containing complex disassembly / Dopamine Neurotransmitter Release Cycle / Golgi Associated Vesicle Biogenesis / zymogen granule membrane / regulated exocytosis / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / regulation of synaptic vesicle priming / storage vacuole / regulation of establishment of protein localization / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to gravity / vesicle-mediated transport in synapse / positive regulation of calcium ion-dependent exocytosis / calcium ion-regulated exocytosis of neurotransmitter / vesicle fusion / eosinophil degranulation / vesicle docking / chloride channel inhibitor activity / secretion by cell / ATP-dependent protein disaggregase activity / SNARE complex / SNAP receptor activity / Cargo recognition for clathrin-mediated endocytosis / regulation of exocytosis / regulation of vesicle-mediated transport / Clathrin-mediated endocytosis / LGI-ADAM interactions / calcium-ion regulated exocytosis / hormone secretion / intra-Golgi vesicle-mediated transport / actomyosin / positive regulation of intracellular protein transport / Golgi to plasma membrane protein transport / neurotransmitter secretion / apical protein localization / positive regulation of hormone secretion / Golgi stack / neurotransmitter receptor internalization / protein localization to membrane / ATP-dependent protein binding / neuron projection terminus / positive regulation of ATP-dependent activity / vesicle-fusing ATPase / regulation of synaptic vesicle recycling / insulin secretion / neurotransmitter transport / syntaxin binding / syntaxin-1 binding / clathrin-coated vesicle / SNARE complex assembly / positive regulation of neurotransmitter secretion / Neutrophil degranulation / endosomal transport / synaptic vesicle priming / regulation of synapse assembly / postsynaptic cytosol / myosin binding / positive regulation of receptor recycling / regulation of neuron projection development / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / exocytosis / associative learning / synaptic vesicle exocytosis / voltage-gated potassium channel activity / protein sumoylation / positive regulation of excitatory postsynaptic potential / synaptic vesicle endocytosis / endomembrane system / calcium channel inhibitor activity / long-term memory / response to glucose 類似検索 - 分子機能 | ||||||
生物種 | Cricetulus griseus (モンゴルキヌゲネズミ) Rattus norvegicus (ドブネズミ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.4 Å | ||||||
データ登録者 | White, K.I. / Zhao, M. / Brunger, A.T. | ||||||
資金援助 | 米国, 1件
| ||||||
引用 | ジャーナル: Elife / 年: 2018 タイトル: Structural principles of SNARE complex recognition by the AAA+ protein NSF. 著者: K Ian White / Minglei Zhao / Ucheor B Choi / Richard A Pfuetzner / Axel T Brunger / 要旨: The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (-ethylmaleimide sensitive ...The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (-ethylmaleimide sensitive factor) and an adaptor protein, SNAP (soluble NSF attachment protein), disassemble the SNARE complex. We report electron-cryomicroscopy structures of the complex of NSF, αSNAP, and the full-length soluble neuronal SNARE complex (composed of syntaxin-1A, synaptobrevin-2, SNAP-25A) in the presence of ATP under non-hydrolyzing conditions at ~3.9 Å resolution. These structures reveal electrostatic interactions by which two αSNAP molecules interface with a specific surface of the SNARE complex. This interaction positions the SNAREs such that the 15 N-terminal residues of SNAP-25A are loaded into the D1 ring pore of NSF via a spiral pattern of interactions between a conserved tyrosine NSF residue and SNAP-25A backbone atoms. This loading process likely precedes ATP hydrolysis. Subsequent ATP hydrolysis then drives complete disassembly. | ||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6mdm.cif.gz | 1.5 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6mdm.ent.gz | 1.2 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6mdm.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
文書・要旨 | 6mdm_validation.pdf.gz | 1.6 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6mdm_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 6mdm_validation.xml.gz | 122.3 KB | 表示 | |
CIF形式データ | 6mdm_validation.cif.gz | 186.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/md/6mdm ftp://data.pdbj.org/pub/pdb/validation_reports/md/6mdm | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-タンパク質 , 5種, 11分子 ABCDEFHIJKL
#1: タンパク質 | 分子量: 85509.227 Da / 分子数: 6 / 由来タイプ: 組換発現 由来: (組換発現) Cricetulus griseus (モンゴルキヌゲネズミ) 遺伝子: NSF / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P18708, vesicle-fusing ATPase #2: タンパク質 | | 分子量: 23512.387 Da / 分子数: 1 / 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: Snap25, Snap / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P60881 #3: タンパク質 | | 分子量: 29634.129 Da / 分子数: 1 / 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: Stx1a, Sap / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P32851 #4: タンパク質 | | 分子量: 12981.304 Da / 分子数: 1 / 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: Vamp2, Syb2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63045 #5: タンパク質 | 分子量: 35598.223 Da / 分子数: 2 / 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: Napa, Snap, Snapa / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P54921 |
---|
-非ポリマー , 2種, 11分子
#6: 化合物 | ChemComp-ATP / #7: 化合物 | |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 |
| ||||||||||||||||||||||||||||||||||||||||||
由来(天然) |
| ||||||||||||||||||||||||||||||||||||||||||
由来(組換発現) |
| ||||||||||||||||||||||||||||||||||||||||||
緩衝液 | pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
緩衝液成分 |
| ||||||||||||||||||||||||||||||||||||||||||
試料 | 濃度: 15 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||||||||
試料支持 | 詳細: Not available | ||||||||||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 293 K / 詳細: Blot for 3.5 seconds before plunging. |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2.7 mm / C2レンズ絞り径: 70 µm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 10 sec. / 電子線照射量: 58 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 2 / 実像数: 5418 |
画像スキャン | 動画フレーム数/画像: 40 / 利用したフレーム数/画像: 2-40 |
-解析
EMソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | 詳細: CTF correction was carried out in Relion with reconstruction step. タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 475680 | ||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 55150 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 3J96 Accession code: 3J96 / Source name: PDB / タイプ: experimental model |