+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8ru2 | ||||||||||||
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タイトル | Structure of the F-actin barbed end bound by formin mDia1 | ||||||||||||
要素 |
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キーワード | STRUCTURAL PROTEIN / actin / formin / Cdc12 / profilin / actin assembly | ||||||||||||
機能・相同性 | 機能・相同性情報 MGMT-mediated DNA damage reversal / negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity ...MGMT-mediated DNA damage reversal / negative regulation of neuron projection regeneration / multicellular organismal locomotion / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / RHOA GTPase cycle / actin nucleation / neuron projection retraction / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / DNA-methyltransferase activity / morphogenesis of a polarized epithelium / RHO GTPases Activate Formins / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction / brahma complex / profilin binding / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / DNA ligation / apical protein localization / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / regulation of microtubule-based process / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / DNA alkylation repair / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / Adherens junctions interactions / tight junction / axon midline choice point recognition / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / maintenance of blood-brain barrier / cortical cytoskeleton / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / synaptic vesicle endocytosis / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / actin filament polymerization / Neutrophil degranulation / axonogenesis / negative regulation of protein binding / methyltransferase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / positive regulation of cell differentiation / adherens junction / sensory perception of sound / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity / ruffle 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 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) Mus musculus (ハツカネズミ) | ||||||||||||
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: 3.49 Å | ||||||||||||
データ登録者 | Oosterheert, W. / Boiero Sanders, M. / Funk, J. / Prumbaum, D. / Raunser, S. / Bieling, P. | ||||||||||||
資金援助 | ドイツ, European Union, 3件
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引用 | ジャーナル: Science / 年: 2024 タイトル: Molecular mechanism of actin filament elongation by formins. 著者: Wout Oosterheert / Micaela Boiero Sanders / Johanna Funk / Daniel Prumbaum / Stefan Raunser / Peter Bieling / 要旨: Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action ...Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action remain unclear. In this work, we present high-resolution cryo-electron microscopy structures of F-actin barbed ends bound by three distinct formins, revealing a common asymmetric formin conformation imposed by the filament. Formation of new intersubunit contacts during actin polymerization sterically displaces formin and triggers its translocation. This "undock-and-lock" mechanism explains how actin-filament growth is coordinated with formin movement. Filament elongation speeds are controlled by the positioning and stability of actin-formin interfaces, which distinguish fast and slow formins. Furthermore, we provide a structure of the actin-formin-profilin ring complex, which resolves how profilin is rapidly released from the barbed end during filament elongation. | ||||||||||||
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 | 8ru2.cif.gz | 346.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8ru2.ent.gz | 271.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8ru2.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 | 8ru2_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8ru2_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 8ru2_validation.xml.gz | 72.3 KB | 表示 | |
CIF形式データ | 8ru2_validation.cif.gz | 104.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ru/8ru2 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/8ru2 | HTTPS FTP |
-関連構造データ
関連構造データ | 19503MC 8rttC 8rtyC 8ru0C 8rv2C C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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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: 3 / 由来タイプ: 組換発現 詳細: Human beta-actin was recombinantly purified from BTI-Tnao38 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 | 分子量: 86469.258 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: Has a N-terminal snap-tag. 由来: (組換発現) Homo sapiens (ヒト), (組換発現) Mus musculus (ハツカネズミ) 遺伝子: MGMT, Diaph1, Diap1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 Star pRARE 参照: UniProt: P16455, UniProt: O08808, methylated-DNA-[protein]-cysteine S-methyltransferase #3: 化合物 | #4: 化合物 | 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 | 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: 7.1 | ||||||||||||||||||||||||||||
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: 67.6 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: 2 / 実像数: 38913 |
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: 1963686 / 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: 3.49 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 150807 / 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 / 詳細: Refinement performed using phenix real-space refine | ||||||||||||||||||||||||||||||||||||||||||||||||
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 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 115.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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