+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19503 | ||||||||||||
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タイトル | Structure of the F-actin barbed end bound by formin mDia1 | ||||||||||||
マップデータ | Sharpened cryo-EM density map of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
試料 |
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キーワード | actin (アクチン) / formin / Cdc12 / profilin (プロフィリン) / actin assembly (アクチン) / STRUCTURAL PROTEIN (タンパク質) | ||||||||||||
機能・相同性 | 機能・相同性情報 negative regulation of neuron projection regeneration / multicellular organismal locomotion / MGMT-mediated DNA damage reversal / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / methylated-DNA-[protein]-cysteine S-methyltransferase ...negative regulation of neuron projection regeneration / multicellular organismal locomotion / MGMT-mediated DNA damage reversal / RHOF GTPase cycle / RHOB GTPase cycle / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / actin nucleation / positive regulation of norepinephrine uptake / neuron projection retraction / cellular response to cytochalasin B / DNA-methyltransferase activity / bBAF complex / npBAF complex / RHO GTPases Activate Formins / protein localization to microtubule / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / profilin binding / morphogenesis of a polarized epithelium / cellular response to histamine / GBAF complex / postsynaptic actin cytoskeleton / protein localization to adherens junction / Formation of annular gap junctions / regulation of G0 to G1 transition / dense body / Gap junction degradation / Tat protein binding / DNA alkylation repair / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of double-strand break repair / DNA ligation / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / regulation of microtubule-based process / regulation of release of sequestered calcium ion into cytosol / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / axon midline choice point recognition / 密着結合 / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / regulation of cytoskeleton organization / apical junction complex / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / cortical cytoskeleton / nitric-oxide synthase binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / 刷子縁 / kinesin binding / ヘルト萼状シナプス / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / actin filament polymerization / Neutrophil degranulation / 軸索誘導 / negative regulation of protein binding / 運動性 / methyltransferase activity / マイクロフィラメント / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / regulation of transmembrane transporter activity / positive regulation of cell differentiation / sensory perception of sound / FCGR3A-mediated phagocytosis 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 | 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
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_19503.map.gz | 398.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19503-v30.xml emd-19503.xml | 27.3 KB 27.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_19503_fsc.xml | 15.9 KB | 表示 | FSCデータファイル |
画像 | emd_19503.png | 95.5 KB | ||
マスクデータ | emd_19503_msk_1.map | 421.9 MB | マスクマップ | |
Filedesc metadata | emd-19503.cif.gz | 8 KB | ||
その他 | emd_19503_additional_1.map.gz emd_19503_half_map_1.map.gz emd_19503_half_map_2.map.gz | 209.9 MB 390.9 MB 390.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19503 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19503 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_19503.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Sharpened cryo-EM density map of the F-actin barbed end bound by the formin mDia1 | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.88 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_19503_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 3D-refined, unsharpened cryo-EM density map of the F-actin...
ファイル | emd_19503_additional_1.map | ||||||||||||
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注釈 | 3D-refined, unsharpened cryo-EM density map of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map 1 of the F-actin barbed...
ファイル | emd_19503_half_map_1.map | ||||||||||||
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注釈 | Unfiltered half map 1 of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map 2 of the F-actin barbed...
ファイル | emd_19503_half_map_2.map | ||||||||||||
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注釈 | Unfiltered half map 2 of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : mDia1-bound F-actin barbed end.
全体 | 名称: mDia1-bound F-actin barbed end. |
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要素 |
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-超分子 #1: mDia1-bound F-actin barbed end.
超分子 | 名称: mDia1-bound F-actin barbed end. / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 詳細: Human beta-actin and mouse mDia1 were purified separately. Both proteins were mixed to assemble the complex prior to cryo-EM grid preparation. |
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-超分子 #2: Actin filament
超分子 | 名称: Actin filament / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-超分子 #3: Mouse mDia1 (FH1FH2C domain)
超分子 | 名称: Mouse mDia1 (FH1FH2C domain) / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
-分子 #1: Actin, cytoplasmic 1, N-terminally processed
分子 | 名称: Actin, cytoplasmic 1, N-terminally processed / タイプ: protein_or_peptide / ID: 1 詳細: Human beta-actin was recombinantly purified from BTI-Tnao38 cells. コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 41.632422 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV ...文字列: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLE K SYELPDGQVI TIGNERFRCP EALFQPSFLG MESAGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEI TALAPSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF UniProtKB: Actin, cytoplasmic 1 |
-分子 #2: Methylated-DNA--protein-cysteine methyltransferase,Protein diapha...
分子 | 名称: Methylated-DNA--protein-cysteine methyltransferase,Protein diaphanous homolog 1 タイプ: protein_or_peptide / ID: 2 / 詳細: Has a N-terminal snap-tag. / コピー数: 2 / 光学異性体: LEVO EC番号: methylated-DNA-[protein]-cysteine S-methyltransferase |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 86.469258 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MASTMDIKLT GEFAMDKDCE MKRTTLDSPL GKLELSGCEQ GLHEIKLLGK GTSAADAVEV PAPAAVLGGP EPLMQATAWL NAYFHQPEA IEEFPVPALH HPVFQQESFT RQVLWKLLKV VKFGEVISYQ QLAALAGNPA ATAAVKTALS GNPVPILIPC H RVVSSSGA ...文字列: MASTMDIKLT GEFAMDKDCE MKRTTLDSPL GKLELSGCEQ GLHEIKLLGK GTSAADAVEV PAPAAVLGGP EPLMQATAWL NAYFHQPEA IEEFPVPALH HPVFQQESFT RQVLWKLLKV VKFGEVISYQ QLAALAGNPA ATAAVKTALS GNPVPILIPC H RVVSSSGA VGGYEGGLAV KEWLLAHEGH RLGKPGLGPA GGSPGGGSGG SEMASLSAVV VAPSVSSSAA VPPAPPLPGD SG TVIPPPP PGMGVPPPPP FGFGVPAAPV LPFGLTPKKV YKPEVQLRRP NWSKFVAEDL SQDCFWTKVK EDRFENNELF AKL TLAFSA QTKTSKAKKD QEGGEEKKSV QKKKVKELKV LDSKTAQNLS IFLGSFRMPY QEIKNVILEV NEAVLTESMI QNLI KQMPE PEQLKMLSEL KEEYDDLAES EQFGVVMGTV PRLRPRLNAI LFKLQFSEQV ENIKPEIVSV TAACEELRKS ENFSS LLEL TLLVGNYMNA GSRNAGAFGF NISFLCKLRD TKSADQKMTL LHFLAELCEN DHPEVLKFPD ELAHVEKASR VSAENL QKS LDQMKKQIAD VERDVQNFPA ATDEKDKFVE KMTSFVKDAQ EQYNKLRMMH SNMETLYKEL GDYFVFDPKK LSVEEFF MD LHNFRNMFLQ AVKENQKRRE TEEKMRRAKL AKEKAEKERL EKQQKREQLI DMNAEGDETG VMDSLLEALQ SGAAFRRK R GPRQVNRKAG CAVTSLLASE LTKDDAMAPG PVKVPKKSEG VPTILEEAKE LVGRASHHHH HH UniProtKB: Methylated-DNA--protein-cysteine methyltransferase, Protein diaphanous homolog 1, Protein diaphanous homolog 1 |
-分子 #3: ADENOSINE-5'-DIPHOSPHATE
分子 | 名称: ADENOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 3 / コピー数: 3 / 式: ADP |
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分子量 | 理論値: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-分子 #4: MAGNESIUM ION
分子 | 名称: MAGNESIUM ION / タイプ: ligand / ID: 4 / コピー数: 3 / 式: MG |
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分子量 | 理論値: 24.305 Da |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.1 構成要素:
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グリッド | モデル: Quantifoil R2/1 / 材質: GOLD / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 90 sec. | |||||||||||||||
凍結 | 凍結剤: ETHANE-PROPANE / チャンバー内湿度: 100 % / チャンバー内温度: 286 K / 装置: FEI VITROBOT MARK IV / 詳細: 3 seconds, force 0.. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / 最大 デフォーカス(公称値): 2.7 µm / 最小 デフォーカス(公称値): 1.2 µm / 倍率(公称値): 81000 |
特殊光学系 | 球面収差補正装置: Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. 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: 15 eV / 詳細: Gatan energy filter. |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
詳細 | 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
撮影 | 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 / 平均電子線量: 67.6 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
-原子モデル構築 1
初期モデル |
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詳細 | Refinement performed using phenix real-space refine | |||||||||
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT | |||||||||
得られたモデル | PDB-8ru2: |