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基本情報
登録情報 | データベース: EMDB / ID: EMD-6102 | |||||||||
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タイトル | Electron cryo-microscopy of DNGR-1 in complex with F-actin | |||||||||
![]() | Reconstruction of DNGR1 in complex with F-actin | |||||||||
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![]() | DNGR-1 / Actin / Damage-associated molecular patterns | |||||||||
機能・相同性 | ![]() positive regulation of cytokine production => GO:0001819 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction ...positive regulation of cytokine production => GO:0001819 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / 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 / 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 / maintenance of blood-brain barrier / cortical cytoskeleton / 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 / 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 / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / EPHB-mediated forward signaling / substantia nigra development / receptor-mediated endocytosis / axonogenesis / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / positive regulation of cell differentiation / 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 / Signaling by high-kinase activity BRAF mutants / DNA Damage Recognition in GG-NER / MAP2K and MAPK activation / B-WICH complex positively regulates rRNA expression / tau protein binding / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / kinetochore / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / nuclear matrix / 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 / nucleosome / Signaling by BRAF and RAF1 fusions / cell-cell junction / Clathrin-mediated endocytosis / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / lamellipodium / presynapse 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.7 Å | |||||||||
![]() | Hanc P / Fujii T / Yamada Y / Huotari J / Schulz O / Ahrens S / Kjaer S / Way M / Namba K / Reis e Sousa C | |||||||||
![]() | ![]() 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. | |||||||||
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構造の表示
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 3.6 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 10.7 KB 10.7 KB | 表示 表示 | ![]() |
画像 | ![]() ![]() | 40.5 KB 4.3 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 329 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 328.6 KB | 表示 | |
XML形式データ | ![]() | 5.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of DNGR1 in complex with F-actin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : F-actin complexed with mouse DNGR-1 extracellular domain
全体 | 名称: F-actin complexed with mouse DNGR-1 extracellular domain |
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要素 |
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-超分子 #1000: F-actin complexed with mouse DNGR-1 extracellular domain
超分子 | 名称: F-actin complexed with mouse DNGR-1 extracellular domain タイプ: sample / ID: 1000 / Number unique components: 1 |
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-分子 #1: DNGR-1
分子 | 名称: DNGR-1 / タイプ: protein_or_peptide / ID: 1 / Name.synonym: CLEC9A / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
組換発現 | 生物種: ![]() ![]() |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 詳細: 25mM Hepes buffer (pH 7.5), 100mM KCl, 1mM MgCl2, 1mM ATP |
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グリッド | 詳細: R0.6/1.0, Quantifoil |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / 装置: FEI VITROBOT MARK II |
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電子顕微鏡法
顕微鏡 | JEOL 3200FSC |
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温度 | 最低: 50 K / 最高: 60 K / 平均: 55 K |
特殊光学系 | 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 - エネルギー下限: 0.0 eV エネルギーフィルター - エネルギー上限: 20.0 eV |
日付 | 2012年12月10日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) 実像数: 774 / 平均電子線量: 20 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 109489 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 1.6 mm / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 60000 |
試料ステージ | 試料ホルダーモデル: JEOL 3200FSC CRYOHOLDER |
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画像解析
CTF補正 | 詳細: Each Particle |
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最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 7.7 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Spider, EMAN / 使用した粒子像数: 73608 |