+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7t7r | |||||||||
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タイトル | Structure of Munc13-1 C1-C2B-MUN-C2C trimer between lipid bilayers | |||||||||
要素 | Protein unc-13 homolog A | |||||||||
キーワード | EXOCYTOSIS / Synaptic Transmission / Munc13 / Membrane Fusion | |||||||||
機能・相同性 | 機能・相同性情報 dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity / innervation / neurotransmitter secretion / regulation of short-term neuronal synaptic plasticity / regulation of amyloid precursor protein catabolic process / syntaxin-1 binding / positive regulation of neurotransmitter secretion / syntaxin binding / synaptic vesicle priming / Golgi-associated vesicle / neuromuscular junction development / spectrin binding / presynaptic active zone / synaptic vesicle exocytosis / calyx of Held / excitatory synapse / amyloid-beta metabolic process / SNARE binding / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / neuromuscular junction / terminal bouton / phospholipid binding / synaptic vesicle membrane / presynapse / presynaptic membrane / cell differentiation / calmodulin binding / neuron projection / protein domain specific binding / axon / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / identical protein binding / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 10 Å | |||||||||
データ登録者 | Grushin, K. / Sindelar, C.V. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2022 タイトル: Munc13 structural transitions and oligomers that may choreograph successive stages in vesicle priming for neurotransmitter release. 著者: Kirill Grushin / R Venkat Kalyana Sundaram / Charles V Sindelar / James E Rothman / 要旨: How can exactly six SNARE complexes be assembled under each synaptic vesicle? Here we report cryo-EM crystal structures of the core domain of Munc13, the key chaperone that initiates SNAREpin ...How can exactly six SNARE complexes be assembled under each synaptic vesicle? Here we report cryo-EM crystal structures of the core domain of Munc13, the key chaperone that initiates SNAREpin assembly. The functional core of Munc13, consisting of C1-C2B-MUN-C2C (Munc13C) spontaneously crystallizes between phosphatidylserine-rich bilayers in two distinct conformations, each in a radically different oligomeric state. In the open conformation (state 1), Munc13C forms upright trimers that link the two bilayers, separating them by ∼21 nm. In the closed conformation, six copies of Munc13C interact to form a lateral hexamer elevated ∼14 nm above the bilayer. Open and closed conformations differ only by a rigid body rotation around a flexible hinge, which when performed cooperatively assembles Munc13 into a lateral hexamer (state 2) in which the key SNARE assembly-activating site of Munc13 is autoinhibited by its neighbor. We propose that each Munc13 in the lateral hexamer ultimately assembles a single SNAREpin, explaining how only and exactly six SNARE complexes are templated. We suggest that state 1 and state 2 may represent two successive states in the synaptic vesicle supply chain leading to "primed" ready-release vesicles in which SNAREpins are clamped and ready to release (state 3). | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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 | 7t7r.cif.gz | 1.1 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7t7r.ent.gz | 923.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7t7r.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 | 7t7r_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7t7r_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 7t7r_validation.xml.gz | 88.6 KB | 表示 | |
CIF形式データ | 7t7r_validation.cif.gz | 140.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/t7/7t7r ftp://data.pdbj.org/pub/pdb/validation_reports/t7/7t7r | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 130895.867 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Unc13a / 細胞株 (発現宿主): ExpiHEK-293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q4KUS2 |
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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: 2D ARRAY / 3次元再構成法: サブトモグラム平均法 |
-試料調製
構成要素 | 名称: 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid bilayers. タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT | ||||||||||||||||||||
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分子量 | 値: 0.13 MDa / 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) | ||||||||||||||||||||
由来(組換発現) | 生物種: Homo sapiens (ヒト) / 細胞: ExpiHEK-293 | ||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 281 K / 詳細: blot for 5 sec before plunging, blot force -1 |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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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): 5000 nm / 最小 デフォーカス(公称値): 3500 nm |
撮影 | 電子線照射量: 3.1 e/Å2 / Avg electron dose per subtomogram: 110 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
電子光学装置 | エネルギーフィルター名称: GIF Quantum LS / エネルギーフィルタースリット幅: 20 eV |
-解析
EMソフトウェア |
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CTF補正 | 詳細: CTF correction was performed during 3D reconstruction in RELION 3.1 タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
対称性 | 点対称性: C3 (3回回転対称) | ||||||||||||||||||||||||||||
3次元再構成 | 解像度: 10 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 42237 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||
EM volume selection | 詳細: Particles were extracted and refined using Warp/M software Num. of tomograms: 62 / Num. of volumes extracted: 70467 | ||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT 詳細: Model for fitting was generated by AlphaFold using the construct's amino acid sequence. Flexible fitting into corresponding density was performed using ISOLDE tool in ChimeraX. The resulting ...詳細: Model for fitting was generated by AlphaFold using the construct's amino acid sequence. Flexible fitting into corresponding density was performed using ISOLDE tool in ChimeraX. The resulting structure was copied and fitted as rigid bodies into the 3D map by "fit in map" function in Chimera. |