+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19503 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||
キーワード | actin / formin / Cdc12 / profilin / actin assembly / STRUCTURAL PROTEIN | ||||||||||||
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 / bBAF complex / RHO GTPases Activate Formins / npBAF complex / postsynaptic actin cytoskeleton organization / brahma complex / nBAF complex / protein localization to adherens junction / profilin binding / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / GBAF complex / dense body / regulation of G0 to G1 transition / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / DNA ligation / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of microtubule-based process / DNA alkylation repair / RHOF GTPase cycle / 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 / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / 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 / cortical cytoskeleton / maintenance of blood-brain barrier / 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 / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / sensory perception of sound / 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 / DNA Damage Recognition in GG-NER 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
| ||||||||||||
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 |
|
-構造の表示
添付画像 |
---|
-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 | |
---|---|---|---|---|
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 |
-検証レポート
文書・要旨 | emd_19503_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_19503_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_19503_validation.xml.gz | 25.4 KB | 表示 | |
CIF形式データ | emd_19503_validation.cif.gz | 33 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19503 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19503 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-マスク #1
ファイル | emd_19503_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Unfiltered half map 1 of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
投影像・断面図 |
| ||||||||||||
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Unfiltered half map 2 of the F-actin barbed end bound by the formin mDia1 | ||||||||||||
投影像・断面図 |
| ||||||||||||
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. |
---|---|
要素 |
|
-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. |
---|
-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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
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:
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
---|---|
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. |
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 |
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 FIELD / 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 |
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 |
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 |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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: |