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基本情報
登録情報 | データベース: EMDB / ID: EMD-25739 | |||||||||
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タイトル | Composite map of Lateral Munc13-1 C1-C2B-MUN-C2C molecule | |||||||||
![]() | Composite 3D map of created in UCSF Chimera by combining two maps from independent, focused 3D classifications using the "vop maximum" command. | |||||||||
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![]() | Synaptic Transmission / Munc13 / Membrane Fusion / EXOCYTOSIS | |||||||||
機能・相同性 | ![]() 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 | ![]() ![]() | |||||||||
手法 | サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 10.0 Å | |||||||||
![]() | Grushin K / Sindelar CV | |||||||||
資金援助 | ![]()
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![]() | ![]() 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 |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 201.2 KB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 13.7 KB 13.7 KB | 表示 表示 | ![]() |
画像 | ![]() | 56.7 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 300.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 299.7 KB | 表示 | |
XML形式データ | ![]() | 5.6 KB | 表示 | |
CIF形式データ | ![]() | 6.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Composite 3D map of created in UCSF Chimera by combining two maps from independent, focused 3D classifications using the "vop maximum" command. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid b...
全体 | 名称: 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid bilayers. |
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要素 |
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-超分子 #1: 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid b...
超分子 | 名称: 2D crystal of Munc13-1 C1-C2B-MUN-C2C domains between two lipid bilayers. タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 130 KDa |
-分子 #1: Protein unc-13 homolog A
分子 | 名称: Protein unc-13 homolog A / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 130.895867 KDa |
組換発現 | 生物種: ![]() |
配列 | 文字列: GPLGSEFMAG ITSALASSTL NNEELKNHVY KKTLQALIYP ISCTTPHNFE VWTATTPTYC YECEGLLWGI ARQGMRCTEC GVKCHEKCQ DLLNADCLQR AAEKSSKHGA EDRTQNIIMV LKDRMKIRER NKPEIFELIQ EVFAVTKSAH TQQMKAVKQS V LDGTSKWS ...文字列: GPLGSEFMAG ITSALASSTL NNEELKNHVY KKTLQALIYP ISCTTPHNFE VWTATTPTYC YECEGLLWGI ARQGMRCTEC GVKCHEKCQ DLLNADCLQR AAEKSSKHGA EDRTQNIIMV LKDRMKIRER NKPEIFELIQ EVFAVTKSAH TQQMKAVKQS V LDGTSKWS AKISITVVCA QGLQAKDKTG SSDPYVTVQV GKTKKRTKTI YGNLNPVWEE NFHFECHNSS DRIKVRVWDE DD DIKSRVK QRFKRESDDF LGQTIIEVRT LSGEMDVWYN LDKRTDKSAV SGAIRLHISV EIKGEEKVAP YHVQYTCLHE NLF HFVTDV QNNGVVKIPD AKGDDAWKVY YDETAQEIVD EFAMRYGVES IYQAMTHFAC LSSKYMCPGV PAVMSTLLAN INAY YAHTT ASTNVSASDR FAASNFGKER FVKLLDQLHN SLRIDLSMYR NNFPASSPER LQDLKSTVDL LTSITFFRMK VQELQ SPPR ASQVVKDCVK ACLNSTYEYI FNNCHELYGR EYQTDPAKKG EVPPEEQGPS IKNLDFWSKL ITLIVSIIEE DKNSYT PCL NQFPQELNVG KISAEVMWSL FAQDMKYAME EHDKHRLCKS ADYMNLHFKV KWLYNEYVAE LPTFKDRVPE YPAWFEP FV IQWLDENEEV SRDFLHGALE RDKKDGFQQT SEHALFSCSV VDVFSQLNQS FEIIKKLECP DPQIVGHYMR RFAKTISN V LLQYADIVSK DFASYCSKEK EKVPCILMNN TQQLRVQLEK MFEAMGGKEL DAEASGTLKE LQVKLNNVLD ELSHVFATS FQPHIEECVR QMGDILSQVK GTGNVPASAC SSVAQDADNV LQPIMDLLDS NLTLFAKICE KTVLKRVLKE LWKLVMNTME RTIVLPPEF LSKLKDHMVR EEAKSLTPKQ CAVVELALDT IKQYFHAGGV GLKKTFLEKS PDLQSLRYAL SLYTQATDLL I KTFVQTQS AQGSGVEDPV GEVSVHVELF THPGTGEQKV TVKVVAANDL KWQTSGIFRP FIEVNIVGPQ LSDKKRKFAT KS KNNSWAP KYNESFQFSL SADAGPECYE LQVCVKDYCF AREDRTVGLA VLQLRELAQR GSAACWLPLG RRIHMDDTGL TVL RILSQR SNDEVAKEFV KLKSDTRSAE EGGAAPAP UniProtKB: Protein unc-13 homolog A, Protein unc-13 homolog A |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | サブトモグラム平均法 |
試料の集合状態 | 2D array |
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試料調製
緩衝液 | pH: 7.4 構成要素:
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 281 K / 装置: FEI VITROBOT MARK IV / 詳細: blot for 5 sec before plunging, blot force -1. |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | 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 |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 3.1 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
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): 5.0 µm / 最小 デフォーカス(公称値): 3.5 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
最終 再構成 | 使用したクラス数: 8 / 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 10.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: RELION (ver. 3.1) 詳細: Combined map of best classes from two 3D classifications in RELION 3.1 of selected regions without angular searches using C6 symmetry expanded dataset. 使用したサブトモグラム数: 72894 |
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抽出 | トモグラム数: 62 / 使用した粒子像数: 36837 詳細: Particles were extracted and refined using Warp/M software |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.1) |
-原子モデル構築 1
詳細 | Model for fitting was generated by AlphaFold using the construct's amino acid sequence. Flexible fitting into 3D map densities was performed using ISOLDE tool in ChimeraX. |
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精密化 | プロトコル: FLEXIBLE FIT |
得られたモデル | ![]() PDB-7t7v: |