+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7p1h | ||||||
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タイトル | Structure of the V. vulnificus ExoY-G-actin-profilin complex | ||||||
要素 |
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キーワード | TOXIN / Bacterial toxin / G-actin / profilin | ||||||
機能・相同性 | 機能・相同性情報 calcium- and calmodulin-responsive adenylate cyclase 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 / morphogenesis of a polarized epithelium / bBAF complex ...calcium- and calmodulin-responsive adenylate cyclase 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 / morphogenesis of a polarized epithelium / 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 / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / tight junction / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / 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 / host cell cytosol / 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 actin filament polymerization / positive regulation of stem cell population maintenance / detection of maltose stimulus / NuA4 histone acetyltransferase complex / maltose transport complex / nitric-oxide synthase binding / positive regulation of epithelial cell migration / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / kinesin binding / carbohydrate transport / brush border / calyx of Held / negative regulation of cell differentiation / carbohydrate transmembrane transporter activity / positive regulation of double-strand break repair via homologous recombination / : / maltose binding / actin monomer binding / maltose transport / maltodextrin transmembrane transport / 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 / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / EPHB-mediated forward signaling / substantia nigra development / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / ATP-binding cassette (ABC) transporter complex / axonogenesis / cell chemotaxis / negative regulation of protein binding / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / regulation of transmembrane transporter activity 類似検索 - 分子機能 | ||||||
生物種 | Escherichia coli (大腸菌) Vibrio vulnificus (バクテリア) Homo sapiens (ヒト) | ||||||
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: 3.9 Å | ||||||
データ登録者 | Belyy, A. / Merino, F. / Raunser, S. | ||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Mechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens. 著者: Alexander Belyy / Felipe Merino / Undine Mechold / Stefan Raunser / 要旨: Bacterial human pathogens secrete initially inactive nucleotidyl cyclases that become potent enzymes by binding to actin inside eukaryotic host cells. The underlying molecular mechanism of this ...Bacterial human pathogens secrete initially inactive nucleotidyl cyclases that become potent enzymes by binding to actin inside eukaryotic host cells. The underlying molecular mechanism of this activation is, however, unclear. Here, we report structures of ExoY from Pseudomonas aeruginosa and Vibrio vulnificus bound to their corresponding activators F-actin and profilin-G-actin. The structures reveal that in contrast to the apo-state, two flexible regions become ordered and interact strongly with actin. The specific stabilization of these regions results in an allosteric stabilization of the nucleotide binding pocket and thereby to an activation of the enzyme. Differences in the sequence and conformation of the actin-binding regions are responsible for the selective binding to either F- or G-actin. Other nucleotidyl cyclase toxins that bind to calmodulin rather than actin undergo a similar disordered-to-ordered transition during activation, suggesting that the allosteric activation-by-stabilization mechanism of ExoY is conserved in these enzymes, albeit the different activator. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7p1h.cif.gz | 308.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7p1h.ent.gz | 252 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7p1h.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 | 7p1h_validation.pdf.gz | 604.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7p1h_full_validation.pdf.gz | 616.8 KB | 表示 | |
XML形式データ | 7p1h_validation.xml.gz | 34.6 KB | 表示 | |
CIF形式データ | 7p1h_validation.cif.gz | 49.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/p1/7p1h ftp://data.pdbj.org/pub/pdb/validation_reports/p1/7p1h | HTTPS FTP |
-関連構造データ
-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: 91467.539 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Escherichia coli (strain K12) (大腸菌), (組換発現) Vibrio vulnificus (バクテリア) 株: K12 / 遺伝子: malE, b4034, JW3994 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 DE3 RIPL / 参照: UniProt: P0AEX9, UniProt: A0A0F6NGV0 |
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#2: タンパク質 | 分子量: 41402.242 Da / 分子数: 1 / Mutation: C272A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACTB / 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 |
#3: タンパク質 | 分子量: 15071.222 Da / 分子数: 1 / 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) / 参照: UniProt: P07737 |
#4: 化合物 | ChemComp-CA / |
#5: 化合物 | ChemComp-ATP / |
研究の焦点であるリガンドがあるか | N |
-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 | 名称: Structure of the V. vulnificus ExoY-G-actin-profilin complex タイプ: COMPLEX / Entity ID: #1-#3 / 由来: MULTIPLE SOURCES |
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分子量 | 実験値: NO |
緩衝液 | pH: 8 |
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: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/1 |
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % |
-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 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1200 nm |
撮影 | 平均露光時間: 2 sec. / 電子線照射量: 60 e/Å2 / 検出モード: SUPER-RESOLUTION / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 6879 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.17.1_3660: / 分類: 精密化 | |||||||||||||||||||||||||||
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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: 1252333 | |||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 342081 / アルゴリズム: FOURIER SPACE / 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 |
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拘束条件 |
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