- EMDB-12237: Subtomogram average reconstruction of humanVPS34 complex II bound... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-12237
タイトル
Subtomogram average reconstruction of humanVPS34 complex II bound to Rab5a on a lipid membrane
マップデータ
A reconstruction of the VPS34 complex II bound to Rab5a on lipid vesicles created by subtomogram averaging. The map was sharpened with LAFTER and resampled onto the map from EMD-12214
試料
複合体: human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a on lipid vesicles
タンパク質・ペプチド: UV radiation resistance-associated gene protein
タンパク質・ペプチド: Phosphatidylinositol 3-kinase catalytic subunit type 3
lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / regulation of endosome size / postsynaptic early endosome / nucleus-vacuole junction / 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 / postsynaptic early endosome / nucleus-vacuole junction / 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 / late endosome to vacuole transport / cellular response to nitrogen starvation / SMAD protein signal transduction / RAB GEFs exchange GTP for GDP on RABs / double-strand break repair via classical nonhomologous end joining / 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 / centrosome cycle / positive regulation of autophagosome maturation / SNARE complex assembly / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / spindle organization / mitotic metaphase chromosome alignment / regulation of synaptic vesicle exocytosis / cytoplasmic pattern recognition receptor signaling pathway / Macroautophagy / 1-phosphatidylinositol-3-kinase activity / RSV-host interactions / lysosome organization / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / positive regulation of exocytosis / axoneme / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / autophagosome membrane / Respiratory syncytial virus (RSV) attachment and entry / phosphatidylinositol phosphate biosynthetic process / mitophagy / chromosome, centromeric region / autophagosome maturation / autophagosome assembly / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / negative regulation of reactive oxygen species metabolic process / neuron development / autophagosome / response to vitamin E / canonical Wnt signaling pathway / regulation of macroautophagy / 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 / somatodendritic compartment / cellular response to epidermal growth factor stimulus / Prevention of phagosomal-lysosomal fusion 類似検索 - 分子機能
UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain ...UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Phosphatidylinositol 3-kinase, Vps34 type / HEAT repeat profile. / HEAT, type 2 / small GTPase Rab1 family profile. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase 類似検索 - ドメイン・相同性
Ras-related protein Rab-5A / Beclin-1 / Phosphatidylinositol 3-kinase catalytic subunit type 3 / Phosphoinositide 3-kinase regulatory subunit 4 / UV radiation resistance-associated gene protein 類似検索 - 構成要素
Sonderforschungsbereich 1035, project number 201302640, project B10
ドイツ
German Research Foundation (DFG)
392923329
ドイツ
Wellcome Trust
103139
英国
Wellcome Trust
203149
英国
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.
#195 - 2016年3月 RAFタンパク質キナーゼ (RAF Protein Kinases) 類似性 (1)
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マップ
ファイル
ダウンロード / ファイル: emd_12237.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
A reconstruction of the VPS34 complex II bound to Rab5a on lipid vesicles created by subtomogram averaging. The map was sharpened with LAFTER and resampled onto the map from EMD-12214
ボクセルのサイズ
X=Y=Z: 1.0665 Å
密度
表面レベル
登録者による: 0.008 / ムービー #1: 0.008
最小 - 最大
-0.08853249 - 0.12369968
平均 (標準偏差)
2.3871984e-05 (±0.005715127)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
320
320
320
Spacing
320
320
320
セル
A=B=C: 341.27997 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.0665
1.0665
1.0665
M x/y/z
320
320
320
origin x/y/z
0.000
0.000
0.000
length x/y/z
341.280
341.280
341.280
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
69
68
88
NX/NY/NZ
82
80
48
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
320
320
320
D min/max/mean
-0.089
0.124
0.000
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添付データ
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ハーフマップ: A reconstruction of the VPS34 complex II bound...
A reconstruction of the VPS34 complex II bound to Rab5a on lipid vesicles created by subtomogram averaging. The even half map, before LAFTER sharpening.
A reconstruction of the VPS34 complex II bound to Rab5a on lipid vesicles created by subtomogram averaging. The odd half map, before LAFTER sharpening.
超分子 #1: human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human...
超分子
名称: human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a on lipid vesicles タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: The subunits were expressed using transient transfection in HEK293T cells. Cells were transfected with three plasmids: pYO1025 (encoding VPS34 and VPS15 in a pCAG backbone), pYO1124 (encoding ...詳細: The subunits were expressed using transient transfection in HEK293T cells. Cells were transfected with three plasmids: pYO1025 (encoding VPS34 and VPS15 in a pCAG backbone), pYO1124 (encoding UVGRAG 1-464 fused to the BATS of ATG14, residues 413-492 in pVAG) and pYO1006 (Beclin1 in pCAG)
由来(天然)
生物種: Homo sapiens (ヒト)
組換発現
生物種: Homo sapiens (ヒト)
分子量
理論値: 392.16 KDa
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分子 #1: UV radiation resistance-associated gene protein
トモグラム数: 105 / 使用した粒子像数: 191196 参照モデル: two gaussian-filtered elipsoids forming a V shape 詳細: To identify particles, subtomograms were aligned to an initial reference consisting of two gaussian-filtered ellipsoids forming a V-shape (Supplementary Fig. 6a, reference). After aligning ...詳細: To identify particles, subtomograms were aligned to an initial reference consisting of two gaussian-filtered ellipsoids forming a V-shape (Supplementary Fig. 6a, reference). After aligning against the V-shape, some subtomograms converged and formed clusters, which indicated the presence of a particle The subtomogram coordinates were cleaned by a minimal distance threshold (distance cut off 8 px, cluster size 2, cluster distance 2 px) and cross correlation cut-off so that 191,169 particles remained.
The model in PDB 7BL1 was built and refined into the subtomogram averaged density map in EMD-12214. This map had the membrane portion of the reconstruction masked out. The reconstruction described in the final reconstruction described above includes the membrane that was masked out in EMD-12214. The final reconstruction was sharpened in LAFTER then resampled onto the density of EMD-12214, for ease of fitting the 7BL1 model.
精密化
空間: REAL / プロトコル: RIGID BODY FIT / 温度因子: 320 / 当てはまり具合の基準: Correlation coefficient