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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-12221 | ||||||||||||||||||
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タイトル | VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex | ||||||||||||||||||
![]() | Sharpened, locally filtered map of VPS26 dimer region of the metazoan retromer:SNX3 assembled on the membrane | ||||||||||||||||||
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機能・相同性 | ![]() vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / nickel cation transmembrane transporter activity / cadmium ion transmembrane transport ...vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / nickel cation transmembrane transporter activity / cadmium ion transmembrane transport / late endosome to Golgi transport / nickel cation transport / protein to membrane docking / solute:proton symporter activity / negative regulation of protein transport / positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / inorganic cation transmembrane transporter activity / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of postsynapse assembly / regulation of dendritic spine maintenance / Metal ion SLC transporters / membrane invagination / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / detection of oxygen / positive regulation of Wnt protein secretion / iron ion transmembrane transporter activity / zinc ion transmembrane transporter activity / manganese ion transport / iron ion transmembrane transport / manganese ion transmembrane transporter activity / regulation of terminal button organization / cobalt ion transport / retromer, cargo-selective complex / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / cadmium ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / intralumenal vesicle formation / iron import into cell / retromer complex binding / negative regulation of late endosome to lysosome transport / copper ion transmembrane transporter activity / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / ferrous iron transmembrane transporter activity / retromer complex / mitochondrial fragmentation involved in apoptotic process / phosphatidylinositol-5-phosphate binding / protein localization to endosome / dopaminergic synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of synapse maturation / voluntary musculoskeletal movement / copper ion transport / negative regulation of viral entry into host cell / basal part of cell / regulation of protein metabolic process / phosphatidylinositol-3-phosphate binding / transcytosis / early phagosome / endocytic recycling / regulation of Wnt signaling pathway / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / regulation of mitochondrion organization / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to iron ion / vacuole / negative regulation of phagocytosis / dendrite morphogenesis / clathrin-coated vesicle / heme biosynthetic process / positive regulation of mitochondrial fission / lysosome organization / cadmium ion binding / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / erythrocyte development / brush border membrane / Iron uptake and transport / response to bacterium / intracellular protein transport / protein destabilization / modulation of chemical synaptic transmission / regulation of protein stability / trans-Golgi network / negative regulation of protein catabolic process / recycling endosome / Wnt signaling pathway / multicellular organismal-level iron ion homeostasis / positive regulation of neuron projection development / negative regulation of inflammatory response / positive regulation of protein catabolic process 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: 9.5 Å | ||||||||||||||||||
![]() | Leneva N / Kovtun O / Morado DR / Briggs JAG / Owen DJ | ||||||||||||||||||
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 | ![]() | 3.9 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 18.8 KB 18.8 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 6.1 KB | 表示 | ![]() |
画像 | ![]() | 97.5 KB | ||
マスクデータ | ![]() | 18.1 MB | ![]() | |
その他 | ![]() ![]() | 17 MB 17 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 351.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 350.3 KB | 表示 | |
XML形式データ | ![]() | 11.7 KB | 表示 | |
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 | ![]() 7bloMC ![]() 7blnC ![]() 7blpC ![]() 7blqC ![]() 7blrC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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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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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened, locally filtered map of VPS26 dimer region of the metazoan retromer:SNX3 assembled on the membrane | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
ファイル | emd_12221_half_map_1.map | ||||||||||||
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注釈 | half-map1 | ||||||||||||
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
ファイル | emd_12221_half_map_2.map | ||||||||||||
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注釈 | half-map2 | ||||||||||||
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 : VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c...
全体 | 名称: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex |
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要素 |
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-超分子 #1: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c...
超分子 | 名称: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4 詳細: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide. |
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由来(天然) | 生物種: ![]() ![]() |
組換発現 | 生物種: ![]() ![]() |
-分子 #1: Vacuolar protein sorting-associated protein 26A
分子 | 名称: Vacuolar protein sorting-associated protein 26A / 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: 34.364617 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: FGPICEIDIV LNDGETRKMA EMKTEDGKVE KHYLFYDGES VSGKVNLAFK QPGKRLEHQG IRIEFVGQIE LFNDKSNTHE FVNLVKELA LPGELTQSRS YDFEFMQVEK PYESYIGANV RLRYFLKVTI VRRLTDLVKE YDLIVHQLAT YPDVNNSIKM E VGIEDCLH ...文字列: FGPICEIDIV LNDGETRKMA EMKTEDGKVE KHYLFYDGES VSGKVNLAFK QPGKRLEHQG IRIEFVGQIE LFNDKSNTHE FVNLVKELA LPGELTQSRS YDFEFMQVEK PYESYIGANV RLRYFLKVTI VRRLTDLVKE YDLIVHQLAT YPDVNNSIKM E VGIEDCLH IEFEYNKSKY HLKDVIVGKI YFLLVRIKIQ HMELQLIKKE ITGIGPSTTT ETETIAKYEI MDGAPVKGES IP IRLFLAG YDPTPTMRDV NKKFSVRYFL NLVLVDEEDR RYFKQQEIIL WRKAPEK |
-分子 #2: Sorting nexin-3
分子 | 名称: Sorting nexin-3 / 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: 17.979393 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: TVADTRRLIT KPQNLNDAYG PPSNFLEIDV SNPQTVGVGR GRFTTYEIRV KTNLPIFKLK ESTVRRRYSD FEWLRSELER ESKVVVPPL PGKAFLRQLP FRGDDGIFDD NFIEERKQGL EQFINKVAGH PLAQNERCLH MFLQDEIIDK SYTPSK |
-分子 #3: C-term (residues 493-54) of Wls (fitted sequence corresponds to h...
分子 | 名称: C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II) タイプ: protein_or_peptide / ID: 3 / 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: 1.221422 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: QPELYLLNTM |
-分子 #4: Vacuolar protein sorting-associated protein 35
分子 | 名称: Vacuolar protein sorting-associated protein 35 / タイプ: protein_or_peptide / ID: 4 / 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: 40.714016 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: QEKLLDEAIQ AVKVQSFQMK RCLDKNKLMD ALKHASNMLG ELRTSMLSPK SYYELYMAIS DELHYLEVYL TDEFAKGRKV ADLYELVQY AGNIIPRLYL LITVGVVYVK SFPQSRKDIL KDLVEMCRGV QHPLRGLFLR NYLLQCTRNI LPDEGEPTDE E TTGDISDS ...文字列: QEKLLDEAIQ AVKVQSFQMK RCLDKNKLMD ALKHASNMLG ELRTSMLSPK SYYELYMAIS DELHYLEVYL TDEFAKGRKV ADLYELVQY AGNIIPRLYL LITVGVVYVK SFPQSRKDIL KDLVEMCRGV QHPLRGLFLR NYLLQCTRNI LPDEGEPTDE E TTGDISDS MDFVLLNFAE MNKLWVRMQH QGHSRDREKR ERERQELRIL VGTNLVRLSQ LEGVNVERYK QIVLTGILEQ VV NCRDALA QEYLMECIIQ VFPDEFHLQT LNPFLRACAE LHQNVNVKNI IIALIDRLAL FAHREDGPGI PADIKLFDIF SQQ VATVIQ SRQDMPSEDV VSLQVSLINL AMKCYP |
-分子 #5: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOX...
分子 | 名称: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE タイプ: ligand / ID: 5 / コピー数: 2 / 式: PIB |
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分子量 | 理論値: 554.374 Da |
-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: 9.5 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: 66271 |
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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) | ![]() |