+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8rty | ||||||||||||
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タイトル | Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom | ||||||||||||
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 F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / MGMT-mediated DNA damage reversal / medial cortex / mitotic actomyosin contractile ring assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / positive regulation of norepinephrine uptake ...F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / MGMT-mediated DNA damage reversal / medial cortex / mitotic actomyosin contractile ring assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / synapse maturation / modification of postsynaptic actin cytoskeleton / regulation of transepithelial transport / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / mitotic actomyosin contractile ring / morphogenesis of a polarized epithelium / DNA-methyltransferase activity / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / npBAF complex / Tat protein binding / brahma complex / structural constituent of postsynaptic actin cytoskeleton / nBAF complex / GBAF complex / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of G0 to G1 transition / dense body / Formation of annular gap junctions / Gap junction degradation / Signaling by ROBO receptors / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of actin filament polymerization / apical protein localization / regulation of double-strand break repair / DNA ligation / regulation of nucleotide-excision repair / adherens junction assembly / mating projection tip / Prefoldin mediated transfer of substrate to CCT/TriC / DNA alkylation repair / barbed-end actin filament capping / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / tight junction / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / regulation of norepinephrine uptake / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of ruffle assembly / 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 synaptic vesicle endocytosis / positive regulation of T cell differentiation / negative regulation of stress fiber assembly / 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 actin filament polymerization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / positive regulation of epithelial cell migration / cell division site / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / actin filament bundle assembly / positive regulation of double-strand break repair via homologous recombination / actin monomer binding / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / EPHB-mediated forward signaling / substantia nigra development / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / phosphotyrosine residue binding / axonogenesis / negative regulation of protein binding / methyltransferase activity / neural tube closure 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) Schizosaccharomyces pombe (分裂酵母) 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: 6.25 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 | 8rty.cif.gz | 442.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8rty.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8rty.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 | 8rty_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8rty_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 8rty_validation.xml.gz | 89.6 KB | 表示 | |
CIF形式データ | 8rty_validation.cif.gz | 128.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/rt/8rty ftp://data.pdbj.org/pub/pdb/validation_reports/rt/8rty | HTTPS FTP |
-関連構造データ
関連構造データ | 19499MC 8rttC 8ru0C 8ru2C 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
-タンパク質 , 3種, 7分子 ABCDEFP
#1: タンパク質 | 分子量: 41632.422 Da / 分子数: 4 / 変異: C272A / 由来タイプ: 組換発現 詳細: Cytoplasmic 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: 77888.820 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Cdc12(FH1FH2) was purified recombinantly from E. coli with a N-terminal snap-tag. 由来: (組換発現) Homo sapiens (ヒト), (組換発現) Schizosaccharomyces pombe (分裂酵母) 遺伝子: MGMT, cdc12, SPAC1F5.04c / プラスミド: pETM-11 詳細 (発現宿主): The construct contains an N-terminal His10-TEV-SNAP tag 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 Star pRARE 参照: UniProt: P16455, UniProt: Q10059, methylated-DNA-[protein]-cysteine S-methyltransferase #4: タンパク質 | | 分子量: 15000.207 Da / 分子数: 1 / 変異: S29C, S71M / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PFN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 Rosetta / 参照: UniProt: P07737 |
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-タンパク質・ペプチド , 1種, 3分子 HIJ
#3: 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: 3 / 由来タイプ: 天然 / 詳細: Phalloidin was bought from sigma. 由来: (天然) Amanita phalloides (タマゴテングタケ) 参照: BIRD: PRD_002366 |
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-非ポリマー , 3種, 11分子
#5: 化合物 | ChemComp-ADP / #6: 化合物 | ChemComp-MG / #7: 化合物 | |
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-詳細
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 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): 3000 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: 63.3 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: 5287 |
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. | ||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 6.25 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 29092 / 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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拘束条件 |
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