+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 9fjm | ||||||||||||
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タイトル | Cryo-EM structure of the phalloidin-bound pointed end of the actin filament. | ||||||||||||
要素 |
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キーワード | STRUCTURAL PROTEIN / actin / phalloidin / filament / pointed end | ||||||||||||
機能・相同性 | 機能・相同性情報 positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / postsynaptic actin cytoskeleton / nBAF complex / protein localization to adherens junction ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / postsynaptic actin cytoskeleton / nBAF complex / protein localization to adherens junction / brahma complex / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / regulation of G0 to G1 transition / Formation of annular gap junctions / dense body / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / RSC-type complex / Prefoldin mediated transfer of substrate to CCT/TriC / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of norepinephrine uptake / positive regulation of T cell differentiation / regulation of synaptic vesicle endocytosis / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / kinesin binding / calyx of Held / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / substantia nigra development / EPHB-mediated forward signaling / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / axonogenesis / platelet aggregation / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / positive regulation of cell differentiation / adherens junction / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity / 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 / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / tau protein binding / Schaffer collateral - CA1 synapse / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / kinetochore / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / nuclear matrix / cytoplasmic ribonucleoprotein granule / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / UCH proteinases / Signaling by BRAF and RAF1 fusions / cell-cell junction / nucleosome / actin cytoskeleton / lamellipodium / Clathrin-mediated endocytosis / presynapse / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) Amanita phalloides (タマゴテングタケ) | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.65 Å | ||||||||||||
データ登録者 | Boiero Sanders, M. / Oosterheert, W. / Hofnagel, O. / Bieling, P. / Raunser, S. | ||||||||||||
資金援助 | ドイツ, European Union, 3件
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引用 | ジャーナル: Nat Commun / 年: 2024 タイトル: Phalloidin and DNase I-bound F-actin pointed end structures reveal principles of filament stabilization and disassembly. 著者: Micaela Boiero Sanders / Wout Oosterheert / Oliver Hofnagel / Peter Bieling / Stefan Raunser / 要旨: Actin filament turnover involves subunits binding to and dissociating from the filament ends, with the pointed end being the primary site of filament disassembly. Several molecules modulate filament ...Actin filament turnover involves subunits binding to and dissociating from the filament ends, with the pointed end being the primary site of filament disassembly. Several molecules modulate filament turnover, but the underlying mechanisms remain incompletely understood. Here, we present three cryo-EM structures of the F-actin pointed end in the presence and absence of phalloidin or DNase I. The two terminal subunits at the undecorated pointed end adopt a twisted conformation. Phalloidin can still bind and bridge these subunits, inducing a conformational shift to a flattened, F-actin-like state. This explains how phalloidin prevents depolymerization at the pointed end. Interestingly, two DNase I molecules simultaneously bind to the phalloidin-stabilized pointed end. In the absence of phalloidin, DNase I binding would disrupt the terminal actin subunit packing, resulting in filament disassembly. Our findings uncover molecular principles of pointed end regulation and provide structural insights into the kinetic asymmetry between the actin filament ends. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 9fjm.cif.gz | 265.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb9fjm.ent.gz | 215.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 9fjm.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 | 9fjm_validation.pdf.gz | 1.8 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 9fjm_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 9fjm_validation.xml.gz | 65.1 KB | 表示 | |
CIF形式データ | 9fjm_validation.cif.gz | 92.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fj/9fjm ftp://data.pdbj.org/pub/pdb/validation_reports/fj/9fjm | HTTPS FTP |
-関連構造データ
関連構造データ | 50506MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 41632.422 Da / 分子数: 4 / 由来タイプ: 組換発現 詳細: Beta-actin recombinantly purified from insect cells. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACTB / プラスミド: p2336 pFL_ACTB_C272A / 細胞株 (発現宿主): BTI-Tnao38 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P60709 #2: タンパク質・ペプチド | タイプ: Peptide-like / クラス: 毒素 / 分子量: 808.899 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: phalloidin from Amanita phalloides. 由来: (天然) Amanita phalloides (タマゴテングタケ) 参照: BIRD: PRD_002366 #3: 化合物 | ChemComp-ADP / #4: 化合物 | ChemComp-MG / #5: 化合物 | ChemComp-PO4 / 研究の焦点であるリガンドがあるか | Y | |
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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: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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分子量 |
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由来(天然) |
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由来(組換発現) | 生物種: Trichoplusia ni (イラクサキンウワバ) / 細胞: BTI-Tnao38 | ||||||||||||||||||||||||||||||
緩衝液 | pH: 7.1 詳細: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP) | ||||||||||||||||||||||||||||||
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 | 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 R2/1 | ||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE-PROPANE / 湿度: 100 % / 凍結前の試料温度: 286 K / 詳細: 3 seconds, force 0. |
-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 詳細: 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
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): 2700 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 0.01 mm / C2レンズ絞り径: 50 µm |
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 | 電子線照射量: 64.6 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 / 実像数: 20393 |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / 詳細: Gatan energy filter. / エネルギーフィルタースリット幅: 15 eV 球面収差補正装置: Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 5200600 / 詳細: Particles picked using SPHIRE-crYOLO. | ||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.65 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 280802 / 詳細: Local Refinement in CryoSPARC. / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 8rtt Accession code: 8rtt / 詳細: actin and phalloidin model / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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