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- EMDB-12220: VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex -
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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-12220 | ||||||||||||||||||
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タイトル | VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex | ||||||||||||||||||
![]() | LAFTER-filtered map of VP35 arch of metazoan retromer:SNX3 complex | ||||||||||||||||||
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![]() | endosomes / coat proteins / membrane trafficking / cargo-sorting / ENDOCYTOSIS | ||||||||||||||||||
機能・相同性 | ![]() positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion / regulation of postsynapse assembly ...positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion / regulation of postsynapse assembly / regulation of terminal button organization / retromer, cargo-selective complex / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / negative regulation of late endosome to lysosome transport / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / retromer complex / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / dopaminergic synapse / voluntary musculoskeletal movement / regulation of protein metabolic process / regulation of synapse maturation / transcytosis / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / regulation of mitochondrion organization / positive regulation of mitochondrial fission / lysosome organization / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / intracellular protein transport / negative regulation of inflammatory response / protein destabilization / modulation of chemical synaptic transmission / regulation of protein stability / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / late endosome / presynapse / endosome / endosome membrane / postsynaptic density / early endosome / lysosome / neuron projection / lysosomal membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / perinuclear region of cytoplasm / extracellular exosome / metal ion binding / cytosol 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: 8.9 Å | ||||||||||||||||||
![]() | Leneva N / Kovtun O | ||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly. 著者: Natalya Leneva / Oleksiy Kovtun / Dustin R Morado / John A G Briggs / David J Owen / ![]() 要旨: Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core ...Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes. | ||||||||||||||||||
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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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 2.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 17.9 KB 17.9 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 6.1 KB | 表示 | ![]() |
画像 | ![]() | 107.4 KB | ||
マスクデータ | ![]() | 18.1 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
その他 | ![]() ![]() | 16.7 MB 16.7 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7blnMC ![]() 7bloC ![]() 7blpC ![]() 7blqC ![]() 7blrC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 764.9 Data #1: Raw image frames for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [micrographs - multiframe] Data #2: Corrected, aligned and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [tilt series] Data #3: Corrected, aligned, dose-filtered and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [tilt series]) |
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リンク
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 | LAFTER-filtered map of VP35 arch of metazoan retromer:SNX3 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.701 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
-マスク #1
ファイル | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half-map1 of VP35 arch of metazoan retromer:SNX3 complex
ファイル | emd_12220_half_map_1.map | ||||||||||||
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注釈 | half-map1 of VP35 arch of metazoan retromer:SNX3 complex | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half-map2 of VP35 arch of metazoan retromer:SNX3 complex
ファイル | emd_12220_half_map_2.map | ||||||||||||
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注釈 | half-map2 of VP35 arch of metazoan retromer:SNX3 complex | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex.
全体 | 名称: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex. |
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要素 |
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-超分子 #1: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex.
超分子 | 名称: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex. タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide. |
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由来(天然) | 生物種: ![]() |
-分子 #1: Vacuolar protein sorting-associated protein 29
分子 | 名称: Vacuolar protein sorting-associated protein 29 / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 20.531705 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQ VIPWGDMASL ALLQRQFDVD ILISGHTHKF EAFEHENKFY INPGSATGAY NALETNIIPS FVLMDIQAST V VTYVYQLI GDDVKVERIE YKKP UniProtKB: Vacuolar protein sorting-associated protein 29 |
-分子 #2: Vacuolar protein sorting-associated protein 35
分子 | 名称: Vacuolar protein sorting-associated protein 35 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 91.816805 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MPTTQQSPQD EQEKLLDEAI QAVKVQSFQM KRCLDKNKLM DALKHASNML GELRTSMLSP KSYYELYMAI SDELHYLEVY LTDEFAKGR KVADLYELVQ YAGNIIPRLY LLITVGVVYV KSFPQSRKDI LKDLVEMCRG VQHPLRGLFL RNYLLQCTRN I LPDEGEPT ...文字列: MPTTQQSPQD EQEKLLDEAI QAVKVQSFQM KRCLDKNKLM DALKHASNML GELRTSMLSP KSYYELYMAI SDELHYLEVY LTDEFAKGR KVADLYELVQ YAGNIIPRLY LLITVGVVYV KSFPQSRKDI LKDLVEMCRG VQHPLRGLFL RNYLLQCTRN I LPDEGEPT DEETTGDISD SMDFVLLNFA EMNKLWVRMQ HQGHSRDREK RERERQELRI LVGTNLVRLS QLEGVNVERY KQ IVLTGIL EQVVNCRDAL AQEYLMECII QVFPDEFHLQ TLNPFLRACA ELHQNVNVKN IIIALIDRLA LFAHREDGPG IPA DIKLFD IFSQQVATVI QSRQDMPSED VVSLQVSLIN LAMKCYPDRV DYVDKVLETT VEIFNKLNLE HIATSSAVSK ELTR LLKIP VDTYNNILTV LKLKHFHPLF EYFDYESRKS MSCYVLSNVL DYNTEIVSQD QVDSIMNLVS TLIQDQPDQP VEDPD PEDF ADEQSLVGRF IHLLRSEDPD QQYLILNTAR KHFGAGGNQR IRFTLPPLVF AAYQLAFRYK ENSKVDDKWE KKCQKI FSF AHQTISALIK AELAELPLRL FLQGALAAGE IGFENHETVA YEFMSQAFSL YEDEISDSKA QLAAITLIIG TFERMKC FS EENHEPLRTQ CALAASKLLK KPDQGRAVST CAHLFWSGRN TDKNGEELHG GKRVMECLKK ALKIANQCMD PSLQVQLF I EILNRYIYFY EKENDAVTIQ VLNQLIQKIR EDLPNLESSE ETEQINKHFH NTLEHLRLRR ESPESEGPIY EGLIL UniProtKB: Vacuolar protein sorting-associated protein 35 |
-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 | 3D array |
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試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 3.0 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 |
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 | 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: 8.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用したサブトモグラム数: 89313 |
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抽出 | トモグラム数: 113 / 使用した粒子像数: 822112 |
最終 角度割当 | タイプ: OTHER |
FSC曲線 (解像度の算出) | ![]() |
-原子モデル構築 1
初期モデル |
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精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT | ||||||||
得られたモデル | ![]() PDB-7bln: |