+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j82 | ||||||
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タイトル | Electron cryo-microscopy of DNGR-1 in complex with F-actin | ||||||
要素 |
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キーワード | MEMBRANE PROTEIN/ADP-BINDING PROTEIN (生体膜) / DNGR-1 / Actin (アクチン) / Recognition of damage-associated molecular patterns / MEMBRANE PROTEIN-ADP-BINDING PROTEIN complex (生体膜) | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of cytokine production => GO:0001819 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton ...positive regulation of cytokine production => GO:0001819 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / GBAF complex / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / Formation of annular gap junctions / dense body / Tat protein binding / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of double-strand break repair / regulation of nucleotide-excision repair / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / RSC-type complex / Adherens junctions interactions / 密着結合 / Sensory processing of sound by outer hair cells of the cochlea / 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 / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / regulation of synaptic vesicle endocytosis / NuA4 histone acetyltransferase complex / apical junction complex / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / 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 / kinesin binding / negative regulation of cell differentiation / ヘルト萼状シナプス / 刷子縁 / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / EPHB-mediated forward signaling / substantia nigra development / 軸索誘導 / receptor-mediated endocytosis / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / 運動性 / マイクロフィラメント / positive regulation of cell differentiation / regulation of transmembrane transporter activity / FCGR3A-mediated phagocytosis / 接着結合 / 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 / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / tau protein binding / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / 動原体 / 血小板 / nuclear matrix / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / UCH proteinases / ヌクレオソーム / Signaling by BRAF and RAF1 fusions / cell-cell junction / マイクロフィラメント / presynapse / lamellipodium / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) 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: 7.7 Å | ||||||
データ登録者 | Hanc, P. / Fujii, T. / Yamada, Y. / Huotari, J. / Schulz, O. / Ahrens, S. / Kjaer, S. / Way, M. / Namba, K. / Reis e Sousa, C. | ||||||
引用 | ジャーナル: Immunity / 年: 2015 タイトル: Structure of the Complex of F-Actin and DNGR-1, a C-Type Lectin Receptor Involved in Dendritic Cell Cross-Presentation of Dead Cell-Associated Antigens. 著者: Pavel Hanč / Takashi Fujii / Salvador Iborra / Yurika Yamada / Jatta Huotari / Oliver Schulz / Susan Ahrens / Svend Kjær / Michael Way / David Sancho / Keiichi Namba / Caetano Reis e Sousa / 要旨: DNGR-1 is a C-type lectin receptor that binds F-actin exposed by dying cells and facilitates cross-presentation of dead cell-associated antigens by dendritic cells. Here we present the structure of ...DNGR-1 is a C-type lectin receptor that binds F-actin exposed by dying cells and facilitates cross-presentation of dead cell-associated antigens by dendritic cells. Here we present the structure of DNGR-1 bound to F-actin at 7.7 Å resolution. Unusually for F-actin binding proteins, the DNGR-1 ligand binding domain contacts three actin subunits helically arranged in the actin filament, bridging over two protofilaments, as well as two neighboring actin subunits along one protofilament. Mutation of residues predicted to mediate ligand binding led to loss of DNGR-1-dependent cross-presentation of dead cell-associated antigens, formally demonstrating that the latter depends on F-actin recognition. Notably, DNGR-1 has relatively modest affinity for F-actin but multivalent interactions allow a marked increase in binding strength. Our findings shed light on modes of actin binding by cellular proteins and reveal how extracellular detection of cytoskeletal components by dedicated receptors allows immune monitoring of loss of cellular integrity. | ||||||
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 | 3j82.cif.gz | 215.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j82.ent.gz | 175.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j82.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j8/3j82 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/3j82 | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 14968.989 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Clec9a, Dngr-1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8BRU4 | ||||
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#2: タンパク質 | 分子量: 41664.484 Da / 分子数: 3 / 由来タイプ: 天然 / 詳細: Human platelet actin / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P60709 #3: 化合物 | ChemComp-CA / | #4: 化合物 | |
-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: FILAMENT / 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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緩衝液 | pH: 7.5 | ||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||
試料支持 | 詳細: R0.6/1.0, Quantifoil | ||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: ETHANE / 湿度: 90 % |
-電子顕微鏡撮影
顕微鏡 | モデル: JEOL 3200FSC / 日付: 2012年12月10日 |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 60000 X / 倍率(補正後): 109489 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 1.6 mm / カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: JEOL 3200FSC CRYOHOLDER / 温度: 55 K / 最高温度: 60 K / 最低温度: 50 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 20 e/Å2 フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) |
電子光学装置 | エネルギーフィルター名称: JEOL Omega filter / エネルギーフィルター 上限: 20 eV / エネルギーフィルター 下限: 0 eV |
-解析
EMソフトウェア |
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CTF補正 | 詳細: Each Particle | ||||||||||||
らせん対称 | 回転角度/サブユニット: 166.6 ° / 軸方向距離/サブユニット: 27.6 Å / らせん対称軸の対称性: C1 | ||||||||||||
3次元再構成 | 手法: IHRSR / 解像度: 7.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 73608 / 詳細: (Single particle--Applied symmetry: C1) / 対称性のタイプ: HELICAL | ||||||||||||
精密化ステップ | サイクル: LAST
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