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基本情報
登録情報 | データベース: PDB / ID: 7aqk | ||||||
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タイトル | Model of the actin filament Arp2/3 complex branch junction in cells | ||||||
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![]() | STRUCTURAL PROTEIN / Actin / Arp2-3 complex / Cytoskeleton | ||||||
機能・相同性 | ![]() podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization ...podosome core / concave side of sperm head / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / peripheral region of growth cone / muscle cell projection membrane / : / meiotic cytokinesis / apical ectoplasmic specialization / basal ectoplasmic specialization / cellular response to rapamycin / lamellipodium organization / spindle localization / skeletal muscle fiber adaptation / cellular response to trichostatin A / leading edge of lamellipodium / Striated Muscle Contraction / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / asymmetric cell division / protein kinase C signaling / hemidesmosome / Arp2/3 complex-mediated actin nucleation / actin filament network formation / podosome ring / orbitofrontal cortex development / actin cap / postsynaptic actin cytoskeleton organization / Regulation of actin dynamics for phagocytic cup formation / negative regulation of axon extension / positive regulation of dendritic spine morphogenesis / maintenance of cell polarity / Clathrin-mediated endocytosis / positive regulation of astrocyte differentiation / : / apical dendrite / : / astrocyte differentiation / positive regulation of fibroblast migration / podosome / positive regulation of synapse assembly / positive regulation of podosome assembly / response to steroid hormone / positive regulation of dendrite morphogenesis / positive regulation of filopodium assembly / smooth muscle cell migration / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / cellular response to platelet-derived growth factor stimulus / mesenchyme migration / cell leading edge / positive regulation of smooth muscle cell migration / filamentous actin / brush border / associative learning / skeletal muscle thin filament assembly / striated muscle thin filament / excitatory synapse / positive regulation of double-strand break repair via homologous recombination / response to immobilization stress / cilium assembly / positive regulation of protein targeting to membrane / glutamate receptor binding / skeletal muscle fiber development / positive regulation of lamellipodium assembly / response to mechanical stimulus / axon terminus / stress fiber / positive regulation of substrate adhesion-dependent cell spreading / cellular response to epidermal growth factor stimulus / cellular response to transforming growth factor beta stimulus / ruffle / cytoskeletal protein binding / positive regulation of neuron differentiation / actin filament polymerization / Neutrophil degranulation / cellular response to nerve growth factor stimulus / meiotic cell cycle / dendritic shaft / secretory granule / filopodium / cell projection / actin filament / positive regulation of protein localization to plasma membrane / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / structural constituent of cytoskeleton / ruffle membrane / cellular response to type II interferon / cell-cell junction / actin filament binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
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 Å | ||||||
![]() | Faessler, F. / Dimchev, G. / Hodirnau, V.V. / Wan, W. / Schur, F.K.M. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. 著者: Florian Fäßler / Georgi Dimchev / Victor-Valentin Hodirnau / William Wan / Florian K M Schur / ![]() ![]() 要旨: The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves ...The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation. | ||||||
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 | 分子: ![]() ![]() |
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ダウンロード
PDBx/mmCIF形式 | ![]() | 790 KB | 表示 | ![]() |
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PDB形式 | ![]() | 505.9 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 1.4 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.4 MB | 表示 | |
XML形式データ | ![]() | 117.6 KB | 表示 | |
CIF形式データ | ![]() | 205 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
-Actin-related protein ... , 7種, 7分子 bacdefg
#1: タンパク質 | 分子量: 44818.711 Da / 分子数: 1 / 由来タイプ: 天然 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. 由来: (天然) ![]() ![]() |
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#2: タンパク質 | 分子量: 47428.031 Da / 分子数: 1 / Mutation: From Bos taurus to Mus Musculus I259V / 由来タイプ: 天然 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. 由来: (天然) ![]() ![]() |
#3: タンパク質 | 分子量: 41016.738 Da / 分子数: 1 Mutation: From Bos taurus to Mus Musculus V43N, Q44K, V58I, D63E, K109N, S154N, N213S, A229V, S256N, S274N, G277V, K278T, L296M, S313G, A216T, R360K 由来タイプ: 天然 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. 由来: (天然) ![]() ![]() |
#4: タンパク質 | 分子量: 34402.043 Da / 分子数: 1 / Mutation: From Bos taurus to Mus Musculus Y84F, S90P / 由来タイプ: 天然 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. 由来: (天然) ![]() ![]() |
#5: タンパク質 | 分子量: 20572.666 Da / 分子数: 1 / Mutation: From Bos taurus to Mus Musculus I24L / 由来タイプ: 天然 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. 由来: (天然) ![]() ![]() |
#6: タンパク質 | 分子量: 19697.047 Da / 分子数: 1 / 由来タイプ: 天然 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. 由来: (天然) ![]() ![]() |
#7: タンパク質 | 分子量: 16295.317 Da / 分子数: 1 / Mutation: From Bos taurus to Mus Musculus D28E / 由来タイプ: 天然 詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...詳細: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. 由来: (天然) ![]() ![]() |
-タンパク質 , 1種, 11分子 hijklmnopqr
#8: タンパク質 | 分子量: 42096.953 Da / 分子数: 11 / 由来タイプ: 天然 詳細: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even ...詳細: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure. 由来: (天然) ![]() ![]() |
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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: CELL / 3次元再構成法: サブトモグラム平均法 |
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試料調製
構成要素 | 名称: Actin Filament Arp2/3 Complex Branch Junction / タイプ: CELL 詳細: Structure obtained from the actin network of extracted and fixed mouse fibroblast lamellipodia Entity ID: all / 由来: NATURAL | ||||||||||||||||||||||||
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由来(天然) | 生物種: ![]() ![]() | ||||||||||||||||||||||||
緩衝液 | pH: 6.1 / 詳細: Adjust to pH 6.1 using NaOH | ||||||||||||||||||||||||
緩衝液成分 |
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試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
試料支持 | 詳細: After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Fibronectin グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/2 | ||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE / 湿度: 80 % / 凍結前の試料温度: 277 K 詳細: Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducials |
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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: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 42000 X / 最大 デフォーカス(公称値): -5.5 nm / 最小 デフォーカス(公称値): -1.75 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: ZEMLIN TABLEAU |
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: 1.21 sec. / 電子線照射量: 2.79 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 詳細: Images were collected in movie-mode at 7 frames per tilt |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 20 eV |
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解析
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 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 14296 詳細: Final reconstruction in RELION was performed after Multiple particle refinement in M version 1.0.9. クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | 手法: Template Matching 詳細: After first classification in Dynamo and re-extraction in Warp 17,146 subvolumes remained. Num. of tomograms: 131 / Num. of volumes extracted: 39300 Reference model: Reference generated from manually selected particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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