+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7bl1 | ||||||||||||||||||||||||
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タイトル | human complex II-BATS bound to membrane-attached Rab5a-GTP | ||||||||||||||||||||||||
要素 |
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キーワード | ENDOCYTOSIS / Rab GTPase / Phosphatidylinositol 3-kinase | ||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / regulation of endosome size / nucleus-vacuole junction / postsynaptic early endosome / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation ...lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / regulation of endosome size / nucleus-vacuole junction / postsynaptic early endosome / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / synaptic vesicle recycling / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / amyloid-beta clearance by transcytosis / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation by host of viral genome replication / modulation by host of viral process / Synthesis of PIPs at the Golgi membrane / regulation of autophagosome assembly / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / engulfment of apoptotic cell / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / regulation of filopodium assembly / suppression by virus of host autophagy / multivesicular body sorting pathway / RAB geranylgeranylation / protein targeting to lysosome / protein targeting to vacuole / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / SMAD protein signal transduction / double-strand break repair via classical nonhomologous end joining / RAB GEFs exchange GTP for GDP on RABs / early phagosome / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / negative regulation of programmed cell death / response to iron(II) ion / TBC/RABGAPs / positive regulation of autophagosome maturation / centrosome cycle / SNARE complex assembly / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / spindle organization / mitotic metaphase chromosome alignment / regulation of synaptic vesicle exocytosis / Macroautophagy / cytoplasmic pattern recognition receptor signaling pathway / 1-phosphatidylinositol-3-kinase activity / lysosome organization / RSV-host interactions / positive regulation of cardiac muscle hypertrophy / positive regulation of exocytosis / p38MAPK cascade / axoneme / Synthesis of PIPs at the plasma membrane / autophagosome membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / Respiratory syncytial virus (RSV) attachment and entry / mitophagy / chromosome, centromeric region / autophagosome maturation / autophagosome assembly / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / response to vitamin E / autophagosome / neuron development / negative regulation of reactive oxygen species metabolic process / regulation of macroautophagy / canonical Wnt signaling pathway / amyloid-beta metabolic process / endomembrane system / cellular defense response / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / phagocytosis / axon terminus / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / Prevention of phagosomal-lysosomal fusion / somatodendritic compartment / cellular response to epidermal growth factor stimulus 類似検索 - 分子機能 | ||||||||||||||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||||||||||||||
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: 9.8 Å | ||||||||||||||||||||||||
データ登録者 | Tremel, S. / Morado, D.R. / Kovtun, O. / Williams, R.L. / Briggs, J.A.G. / Munro, S. / Ohashi, Y. / Bertram, J. / Perisic, O. | ||||||||||||||||||||||||
資金援助 | 英国, 7件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes. 著者: Shirley Tremel / Yohei Ohashi / Dustin R Morado / Jessie Bertram / Olga Perisic / Laura T L Brandt / Marie-Kristin von Wrisberg / Zhuo A Chen / Sarah L Maslen / Oleksiy Kovtun / Mark Skehel / ...著者: Shirley Tremel / Yohei Ohashi / Dustin R Morado / Jessie Bertram / Olga Perisic / Laura T L Brandt / Marie-Kristin von Wrisberg / Zhuo A Chen / Sarah L Maslen / Oleksiy Kovtun / Mark Skehel / Juri Rappsilber / Kathrin Lang / Sean Munro / John A G Briggs / Roger L Williams / 要旨: The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal ...The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L). The endosomal GTPase Rab5 binds complex II, but the mechanism of VPS34 activation by Rab5 has remained elusive, and no GTPase is known to bind complex I. Here we show that Rab5a-GTP recruits endocytic complex II to membranes and activates it by binding between the VPS34 C2 and VPS15 WD40 domains. Electron cryotomography of complex II on Rab5a-decorated vesicles shows that the VPS34 kinase domain is released from inhibition by VPS15 and hovers over the lipid bilayer, poised for catalysis. We also show that the GTPase Rab1a, which is known to be involved in autophagy, recruits and activates the autophagy-specific complex I, but not complex II. Both Rabs bind to the same VPS34 interface but in a manner unique for each. These findings reveal how VPS34 complexes are activated on membranes by specific Rab GTPases and how they are recruited to unique cellular locations. | ||||||||||||||||||||||||
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 | 7bl1.cif.gz | 501.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7bl1.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 7bl1.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 | 7bl1_validation.pdf.gz | 939.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7bl1_full_validation.pdf.gz | 946.7 KB | 表示 | |
XML形式データ | 7bl1_validation.xml.gz | 67.7 KB | 表示 | |
CIF形式データ | 7bl1_validation.cif.gz | 114.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/bl/7bl1 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7bl1 | 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
-タンパク質 , 5種, 5分子 AAABBBCCCEEEDDD
#1: タンパク質 | 分子量: 78258.836 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UVRAG / 細胞株 (発現宿主): HEK293T / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9P2Y5 |
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#2: タンパク質 | 分子量: 101680.328 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PIK3C3, VPS34 / 細胞株 (発現宿主): expi293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8NEB9, phosphatidylinositol 3-kinase |
#3: タンパク質 | 分子量: 154790.391 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PIK3R4, VPS15 / 細胞株 (発現宿主): expi293F / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: Q99570, non-specific serine/threonine protein kinase |
#4: タンパク質 | 分子量: 51953.102 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BECN1, GT197 / 細胞株 (発現宿主): expi293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q14457 |
#6: タンパク質 | 分子量: 18769.314 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAB5A, RAB5 発現宿主: Escherichia coli str. K-12 substr. DH10B (大腸菌) 参照: UniProt: P20339, small monomeric GTPase |
-タンパク質・ペプチド , 1種, 1分子 FFF
#5: タンパク質・ペプチド | 分子量: 1581.727 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): expi293F / 発現宿主: Homo sapiens (ヒト) |
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-非ポリマー , 2種, 2分子
#7: 化合物 | ChemComp-GTP / |
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#8: 化合物 | ChemComp-MG / |
-詳細
研究の焦点であるリガンドがあるか | N |
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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: 3D 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 |
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分子量 | 値: 392615 kDa/nm / 実験値: NO | ||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 8 | ||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 6.2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||
試料支持 | 詳細: Quorum SC7620 / グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil | ||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 316 K / 詳細: Blot force 20, blot time 6 s |
-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 / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 5000 nm / 最小 デフォーカス(公称値): 2000 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 0.55 sec. / 電子線照射量: 2.99 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 |
画像スキャン | 横: 6000 / 縦: 4000 |
-解析
ソフトウェア | 名称: REFMAC / バージョン: 5.8.0272 / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 9.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 26979 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 105 / Num. of volumes extracted: 191196 / Reference model: two Gaussian filtered elipsoids | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 320 / プロトコル: FLEXIBLE FIT / 空間: REAL / Target criteria: correlation 詳細: An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. The model was refined in REFMAC with self- ...詳細: An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. The model was refined in REFMAC with self-restraints (4.3) and restraints to 3MJH, 4DDP and 3IHY. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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精密化 | 解像度: 9.8→234.63 Å / Cor.coef. Fo:Fc: 0.954 / WRfactor Rwork: 0.1573 / SU B: 303.369 / SU ML: 1.88 / Average fsc overall: 0.9814 / Average fsc work: 0.9814 詳細: Hydrogens have been used if present in the input file
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溶媒の処理 | 溶媒モデル: BABINET MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 320.935 Å2
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拘束条件 |
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LS精密化 シェル | Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %
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