+データを開く
-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 | ||||||||||||||||||
マップデータ | Sharpened, locally filtered map of VPS26 dimer region of the metazoan retromer:SNX3 assembled on the membrane | ||||||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 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 / nickel cation transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / late endosome to Golgi 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 / nickel cation transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / cadmium ion transmembrane transport / nickel cation transport / solute:proton symporter activity / protein to membrane docking / negative regulation of protein transport / neurotransmitter receptor transport, endosome to plasma membrane / Metal ion SLC transporters / membrane invagination / inorganic cation transmembrane transporter activity / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / zinc ion transmembrane transporter activity / manganese ion transport / tubular endosome / positive regulation of Wnt protein secretion / detection of oxygen / mitochondrion to lysosome vesicle-mediated transport / regulation of terminal button organization / cobalt ion transport / cadmium ion transmembrane transporter activity / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / manganese ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / regulation of postsynapse assembly / intralumenal vesicle formation / iron import into cell / positive regulation of locomotion involved in locomotory behavior / copper ion transmembrane transporter activity / iron ion transmembrane transporter activity / retromer complex binding / negative regulation of lysosomal protein catabolic process / negative regulation of late endosome to lysosome transport / iron ion transmembrane transport / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / vesicle-mediated transport in synapse / ferrous iron transmembrane transporter activity / retromer complex / phosphatidylinositol-5-phosphate binding / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / copper ion transport / voluntary musculoskeletal movement / negative regulation of viral entry into host cell / dopaminergic synapse / basal part of cell / regulation of protein metabolic process / D1 dopamine receptor binding / regulation of synapse maturation / transcytosis / early phagosome / endocytic recycling / phosphatidylinositol-3-phosphate binding / regulation of Wnt signaling pathway / retrograde transport, endosome to Golgi / regulation of mitochondrion organization / vacuole / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of protein localization to cell periphery / response to iron ion / 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 / regulation of macroautophagy / erythrocyte development / intracellular protein transport / Iron uptake and transport / response to bacterium / brush border membrane / protein destabilization / trans-Golgi network / negative regulation of protein catabolic process / modulation of chemical synaptic transmission / regulation of protein stability / recycling endosome / : / Wnt signaling pathway / positive regulation of neuron projection development / negative regulation of inflammatory response / multicellular organismal-level iron ion homeostasis 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Mus musculus (ハツカネズミ) / Homo sapiens (ヒト) | ||||||||||||||||||
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 | ||||||||||||||||||
データ登録者 | Leneva N / Kovtun O / Morado DR / Briggs JAG / Owen DJ | ||||||||||||||||||
資金援助 | 英国, 5件
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引用 | ジャーナル: Sci Adv / 年: 2021 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 |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_12221.map.gz | 3.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12221-v30.xml emd-12221.xml | 18.8 KB 18.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12221_fsc.xml | 6.1 KB | 表示 | FSCデータファイル |
画像 | emd_12221.png | 97.5 KB | ||
マスクデータ | emd_12221_msk_1.map | 18.1 MB | マスクマップ | |
その他 | emd_12221_half_map_1.map.gz emd_12221_half_map_2.map.gz | 17 MB 17 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12221 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12221 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12221_validation.pdf.gz | 351.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12221_full_validation.pdf.gz | 350.3 KB | 表示 | |
XML形式データ | emd_12221_validation.xml.gz | 11.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12221 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12221 | 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 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10633 (タイトル: Cryo-electron tomography of the metazoan membrane-assembled retromer:SNX3 coat containing Wls cargo motif 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]) |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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-マップ
ファイル | ダウンロード / ファイル: emd_12221.map.gz / 形式: CCP4 / 大きさ: 18.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened, locally filtered map of VPS26 dimer region of the metazoan retromer:SNX3 assembled on the membrane | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | emd_12221_msk_1.map | ||||||||||||
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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 |
-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: Mus musculus (ハツカネズミ) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-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: Homo sapiens (ヒト) |
分子量 | 理論値: 34.364617 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
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: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 17.979393 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
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: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 1.221422 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
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: Homo sapiens (ヒト) |
分子量 | 理論値: 40.714016 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
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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解析 | サブトモグラム平均法 |
試料の集合状態 | 3D array |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-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: FIELD EMISSION GUN |
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 |
-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) |